https://ringo.ams.stonybrook.edu/api.php?action=feedcontributions&user=Rizzo&feedformat=atomRizzo_Lab - User contributions [en]2022-11-27T18:05:30ZUser contributionsMediaWiki 1.29.0https://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=152132022-2023 AMS-532 Fall-Spring2022-11-14T16:37:06Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || Liu et al; Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. ''Frontiers in Genetics'' '''2021''', ''12'', Article 655536<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || Watson et al; The evolutionary dynamics and fitness landscape of clonal hematopoiesis. ''Science'' '''2020''', ''367'', 1449<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || Smaers et al; Brain size expansion in primates and humans is explained by a selective modular expansion of the cortico-cerebellar system. ''Cortex'' '''2019''', ''118'', 292-305<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || Wiegand et al; Consequences of spatial patterns for coexistence in species-rich plant communities. ''Nature Ecology & Evolution'' '''2021''', ''5'', 965-973<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || Strey; Estimation of parameters from time traces originating from an Ornstein-Uhlenbeck process. ''PHYSICAL REVIEW E'' '''2019''', ''100'', -62142<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || Robert et al; Resource-efficient quantum algorithm for protein folding. ''npj Quantum Information'' '''2021''', ''38''<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || Luttens et al; Ultralarge Virtual Screening Identifies SARS-CoV‐2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses. ''JACS'' '''2022''', ''144'', 2905−2920<br />
|-<br />
<br />
| 2022.11.09 Wed || No Class || -- || -- || No Class<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || Li et al; Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction. ''Nature Biotechnology'' '''2022''', https://doi.org/10.1038/s41587-022-01476-y<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Moy, Olivia & Genovese, Stacy || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=152112022-2023 AMS-532 Fall-Spring2022-11-08T15:00:49Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || Liu et al; Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. ''Frontiers in Genetics'' '''2021''', ''12'', Article 655536<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || Watson et al; The evolutionary dynamics and fitness landscape of clonal hematopoiesis. ''Science'' '''2020''', ''367'', 1449<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || Smaers et al; Brain size expansion in primates and humans is explained by a selective modular expansion of the cortico-cerebellar system. ''Cortex'' '''2019''', ''118'', 292-305<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || Wiegand et al; Consequences of spatial patterns for coexistence in species-rich plant communities. ''Nature Ecology & Evolution'' '''2021''', ''5'', 965-973<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || Strey; Estimation of parameters from time traces originating from an Ornstein-Uhlenbeck process. ''PHYSICAL REVIEW E'' '''2019''', ''100'', -62142<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || Robert et al; Resource-efficient quantum algorithm for protein folding. ''npj Quantum Information'' '''2021''', ''38''<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || Luttens et al; Ultralarge Virtual Screening Identifies SARS-CoV‐2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses. ''JACS'' '''2022''', ''144'', 2905−2920<br />
|-<br />
<br />
| 2022.11.09 Wed || No Class || -- || -- || No Class<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || TBD<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Moy, Olivia & Genovese, Stacy || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=152102022-2023 AMS-532 Fall-Spring2022-11-08T15:00:18Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || Liu et al; Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. ''Frontiers in Genetics'' '''2021''', ''12'', Article 655536<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || Watson et al; The evolutionary dynamics and fitness landscape of clonal hematopoiesis. ''Science'' '''2020''', ''367'', 1449<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || Smaers et al; Brain size expansion in primates and humans is explained by a selective modular expansion of the cortico-cerebellar system. ''Cortex'' '''2019''', ''118'', 292-305<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || Wiegand et al; Consequences of spatial patterns for coexistence in species-rich plant communities. ''Nature Ecology & Evolution'' '''2021''', ''5'', 965-973<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || Strey; Estimation of parameters from time traces originating from an Ornstein-Uhlenbeck process. ''PHYSICAL REVIEW E'' '''2019''', ''100'', -62142<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || Robert et al; Resource-efficient quantum algorithm for protein folding. ''npj Quantum Information'' '''2021''', ''38''<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || Luttens et al; Ultralarge Virtual Screening Identifies SARS-CoV‐2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses. ''JACS'' '''2022''', ''144'', 2905−2920<br />
|-<br />
<br />
| 2022.11.09 Wed || No Class || -- || -- || --<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || TBD<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Moy, Olivia & Genovese, Stacy || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=152072022 AMS-535 Fall2022-11-02T17:49:38Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Mannaf, Aniqa mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.10.10 Mon</center><br />
|| <br />
*''No Class: Fall Break''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
<br />
| <center>2022.10.12 Wed</center><br />
|| <br />
*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. No online presentation for paper #1<br />
<br><br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
|-<br />
<br />
| <center>2022.10.17 Mon</center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
<br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
||<br />
*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Boysan, Brock mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
<br />
| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Mannaf, Aniqa mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
1. No online presentation for paper #1<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Henderson, Max mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Bauer, Jack mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Urena, Jailene mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. No online presentation for paper #2<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=152062022 AMS-535 Fall2022-11-02T17:48:33Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Mannaf, Aniqa mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
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|- style="background:peachpuff"<br />
| <center>2022.10.10 Mon</center><br />
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*''No Class: Fall Break''<br />
||<center>-</center><br />
||<center>-</center><br />
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|-<br />
<br />
<br />
| <center>2022.10.12 Wed</center><br />
|| <br />
*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 No online presentation for paper #1]<br />
<br><br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
|-<br />
<br />
| <center>2022.10.17 Mon</center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
<br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
||<br />
*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Boysan, Brock mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
<br />
| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Mannaf, Aniqa mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
1. No online presentation for paper #1<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Henderson, Max mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Bauer, Jack mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Urena, Jailene mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. No online presentation for paper #2]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=152052022 AMS-535 Fall2022-11-02T17:45:12Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Mannaf, Aniqa mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.10.10 Mon</center><br />
|| <br />
*''No Class: Fall Break''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
<br />
| <center>2022.10.12 Wed</center><br />
|| <br />
*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 No online presentation for first paper]<br />
<br><br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
|-<br />
<br />
| <center>2022.10.17 Mon</center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
<br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
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*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Glukhov, Ernest mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
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<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
<br />
| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Mannaf, Aniqa mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
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|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Henderson, Max mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Bauer, Jack mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Urena, Jailene mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.mp4 Glukhov, Ernest mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=152042022 AMS-535 Fall2022-11-02T17:44:10Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Mannaf, Aniqa mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.10.10 Mon</center><br />
|| <br />
*''No Class: Fall Break''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
<br />
| <center>2022.10.12 Wed</center><br />
|| <br />
*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 no presentation for first paper mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
|-<br />
<br />
| <center>2022.10.17 Mon</center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
<br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
||<br />
*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Glukhov, Ernest mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
<br />
| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Mannaf, Aniqa mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Henderson, Max mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Bauer, Jack mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Urena, Jailene mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.mp4 Glukhov, Ernest mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=152032022 AMS-535 Fall2022-11-02T17:38:59Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Mannaf, Aniqa mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
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|- style="background:peachpuff"<br />
| <center>2022.10.10 Mon</center><br />
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*''No Class: Fall Break''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
<br />
| <center>2022.10.12 Wed</center><br />
|| <br />
*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 Carter, Vanessa mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
|-<br />
<br />
| <center>2022.10.17 Mon</center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
<br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
||<br />
*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Glukhov, Ernest mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Outhwaite, Ian mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Marr, Douglas mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Dar, Nauroz mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
<br />
| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Mannaf, Aniqa mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Biju, Bismi mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Kakade, Yogesh mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Becker, Kindra mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Snyders, Hayden mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Cheung, Andrew mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Cordero, Ricardo mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Chong, Jiyun mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Moy, Olivia mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Henderson, Max mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Bauer, Jack mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Kaur, Gurlin mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Sayed, Aaliya mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Urena, Jailene mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.mp4 Glukhov, Ernest mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=152022022-2023 AMS-532 Fall-Spring2022-11-02T17:20:17Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || Liu et al; Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. ''Frontiers in Genetics'' '''2021''', ''12'', Article 655536<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || Watson et al; The evolutionary dynamics and fitness landscape of clonal hematopoiesis. ''Science'' '''2020''', ''367'', 1449<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || Smaers et al; Brain size expansion in primates and humans is explained by a selective modular expansion of the cortico-cerebellar system. ''Cortex'' '''2019''', ''118'', 292-305<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || Wiegand et al; Consequences of spatial patterns for coexistence in species-rich plant communities. ''Nature Ecology & Evolution'' '''2021''', ''5'', 965-973<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || Strey; Estimation of parameters from time traces originating from an Ornstein-Uhlenbeck process. ''PHYSICAL REVIEW E'' '''2019''', ''100'', -62142<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || Robert et al; Resource-efficient quantum algorithm for protein folding. ''npj Quantum Information'' '''2021''', ''38''<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || Luttens et al; Ultralarge Virtual Screening Identifies SARS-CoV‐2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses. ''JACS'' '''2022''', ''144'', 2905−2920<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || TBD<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || TBD<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Genovese, Stacy || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=AMS-531_Laboratory_Rotations_in_Computational_Biology&diff=15120AMS-531 Laboratory Rotations in Computational Biology2022-10-21T15:57:16Z<p>Rizzo: /* Rotation Schedules */</p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]<br />
|-<br />
| '''Course No.''' || AMS-531 <br />
|-<br />
| '''Location/Time''' || Individual <br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' In this course, first year PhD students spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology faculty. At the end of each rotation, students give a presentation of their lab activities and accomplishments. The primary goal of rotations is to help students choose a research advisor and to help faculty members choose students. Students register for AMS 531 in both the Fall and Spring semesters of the first year. Fall and Spring, 0 - 3 credits, S/U grading. Crosslisted with PHY 584.<br />
<br />
<br />
'''Learning Objectives:'''<br />
<br />
*(1) Learn how research is conducted at a "very high research" University. <br />
*(2) Actively participate in research of three Computational Biology faculty. <br />
*(3) Gain experience working as a part of a team. <br />
*(4) Learn to use cutting edge research tools in Computational Biology.<br />
*(5) Explore research projects that could lead to dissertation work. <br />
*(6) Gain experience giving group-meeting presentations on lab activities and accomplishments. <br />
<br />
<br />
'''Lab Rotation Goals:''' The goal of "Lab Rotations" is for PhD students in the AMS Computational Biology Track to learn in detail what and how research is conducted in at least three groups over the Fall and Spring semesters of the first year. Note that Lab Rotations are required of all PhD students. For Masters students, Lab Rotations are optional and may be pursued with interested faculty on a case-by-case basis. At the end of each rotation, students give a brief synopsis (~15 minutes) of their lab activities and accomplishments. The goal of the rotations is to help students choose a research advisor and to help faculty members choose students. Students should consult the AMS compbio track webpage at http://www.ams.sunysb.edu/CB/CBOverview.shtml, talk with senior Stony Brook students, and contact potential PI's in an effort to narrow down a list to 3-4 potential laboratories. Depending on availability, and in conjunction with the AMS-531 instructor, three rotations are then scheduled for the following dates:<br />
<br />
<br />
*Rotation 1: ~ Sep 29 – Nov 28 (Fall)<br />
*Rotation 2: ~ Dec 01 – Feb 27 (Fall-Spring)<br />
*Rotation 3: ~ Mar 02 – May 01 (Spring)<br />
<br />
<br />
'''Lab Rotation Guidelines:''' The goal of lab rotations is to help students choose a research advisor and to help faculty members choose students. In particular, faculty members use rotations as a way to help gauge how a student will work in a laboratory setting and if they would be a productive team member of the lab. With this objective in mind it is important to consider the following points when doing each rotation.<br />
<br />
<br />
*Become fully engaged in the lab during your rotation. Make arrangements with the group leader to have a desk or other place at which you can work and be sure to go to the lab everyday. If you need to work on class assignments do your homework in the lab. Students that rarely show up leave a less than favorable impression. <br />
<br />
*Show interest in the lab's research. Ask questions. <br />
<br />
*Read key papers from the lab. Become well-acquainted with tools being used in the group. <br />
<br />
*Be proactive in communicating with others in the lab. Ask for help and guidance to get started. <br />
<br />
*Attend lab meetings. Ask questions. <br />
<br />
*Be proactive in asking your rotation advisor to discuss with you research projects which could be pursued should you join the group permanently. <br />
<br />
*Keep in mind that faculty members must devote considerable time, effort, as well as provide financial assistance when they commit to becoming an advisor to a student. Thus, faculty members want to be sure that before they make such a commitment a student has good work habits, can communicate, is easy to work with, is interested in the lab's research, and wants to succeed in graduate school. Lab rotations can be used to show to potential advisors you have such qualities.<br />
<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br />
<br />
== Rotation Schedules==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''Academic Year''' <br />
| '''Participant''' <br />
| '''Track'''<br />
| '''Rotation 1''' (~ Sep 29 to Nov 28)<br />
| '''Rotation 2''' (~ Dec 01 to Feb 27)<br />
| '''Rotation 3''' (~ Mar 02 to May 01)<br />
|-<br />
|-<br />
| 2023-2022 || Cheung, Andrew || PhD - AMS || MacCarthy / Damagh || TBD || TBD<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2022-2021 || Carter, Simon || PhD - AMS || La Camera || Wei || Strey<br />
|-<br />
| 2022-2021 || Dean, Noah || PhD - AMS || Strey || Lynch || Balazi<br />
|-<br />
| 2022-2021 || Feltman, Scott || PhD - AMS || Strey || Koo || MacCarthy / Damaghi<br />
|-<br />
| 2022-2021 || Grange, Daniel || PhD - AMS || Sandhu || Sandhu || Sandhu<br />
|-<br />
| 2022-2021 || Song, Joon-Hyun || PhD - AMS || Kosakov || Koo || MacCarthy<br />
|-<br />
| 2022-2021 || Delamonica, Brenda || MS - AMS || Koo || Balazi || Strey<br />
|-<br />
| 2022-2021 || Chowdury, FIrst || MS - AMS || Rest || Rest || Rest<br />
|-<br />
| 2022-2021 || Huffstutler, Thomas || MS - AMS || Kosakov || - || Koo<br />
|-<br />
| 2022-2021 || Jiang, Yuhe || MS - AMS || MacCarthy || - || -<br />
|-<br />
| 2022-2021 || Genovese, Stacy || MS - AMS || Simmerling || - || -<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2021-2020 || Hall, Carole || MS - AMS || Green || Lynch || Title<br />
|-<br />
| 2021-2020 || Rajesh, Chandana || MS - AMS || Koo || Koo || -<br />
|-<br />
| 2021-2020 || Steier, Josh || MS - AMS || Deng || Simmerling || Rizzo<br />
|-<br />
| 2021-2020 || Chung, So Young || MS - AMS || MacCarthy || - || -<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2020-2019 || Samoilova, Khristina || PhD - AMS || Brinkman || Mujica-Parodi || Zador<br />
|-<br />
| 2020-2019 || Stepanenko, Darya || PhD - AMS || Dill || Simmerling || Rizzo<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2019-2018 || Ashizawa, Ryota|| PhD - AMS || Simmerling || Kozakov || -<br />
|-<br />
| 2019-2018 || Crosser, Jacob || PhD - AMS || Brinkman || Balazi || -<br />
|-<br />
| 2019-2018 || Bickel, John|| PhD - CHE || Rizzo || Simmerling || -<br />
|-<br />
| 2019-2018 || Wang,Yuzhang || PhD - CHE || Simmerling || Rizzo || -<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2018-2017 || Spyrou, Ioanna || PhD - AMS || Green || Sandhu || Park<br />
|-<br />
| 2018-2017 ||Talis,Emma || PhD - AMS || MacCarthy || Balazsi || Green<br />
|-<br />
| 2018-2017 || Manathunga, Lakshan || PhD - CHE || Simmerling || Rizzo || Kozakov<br />
|-<br />
| 2018-2017 || Taouil, Adam || PhD - CHE || Dill || Simmerling || Rizzo<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2017-2016 || Cao, Xin || PhD - AMS || Coutsias || Tannenbaum || Balazi<br />
|-<br />
| 2017-2016 || Fallon, Zachary || PhD - CHE || Rizzo || Simmerling || Kosakov<br />
|-<br />
| 2017-2016 || Nassar, Roy || PhD - CHE || Dill || Rizzo || Simmerling<br />
|-<br />
| 2017-2016 || O'Connell, Daniel || PhD - AMS || Dill || Rizzo || Futcher<br />
|-<br />
| 2017-2016 || Telehany, Stephen || PhD - CHE || Simmerling || Raleigh || Rizzo<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2016-2015 || Awwa, Monaf || PhD - CHE || Rizzo || Simmerling || Kosakov<br />
|-<br />
| 2016-2015 ||Banisafar, Sahar|| PhD - AMS || Tannenbaum || Kosakov || Coutsias<br />
|-<br />
| 2016-2015 || Guo, Haoyue || PhD - CHE || Balazi || MacCarthy || Simmerling<br />
|-<br />
| 2016-2015 || Jiang, Beilei || PhD - CHE || Simmerling || Rizzo || Kosakov<br />
|-<br />
| 2016-2015 || Tuznik, Stanley || PhD - AMS || Tannenbaum || Kosakov || Rizzo<br />
|-<br />
| 2016-2015 || Hu, Yu || MS - AMS|| TBD || TBD || Balazi<br />
|-<br />
| 2016-2015 || Shapiro, Maxwell || MS - AMS || Rest || MacCarthy || Patro<br />
|-<br />
| 2016-2015 || Xue, Jing || MS - AMS || Kosakov || TBD || TBD<br />
|-<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2015-2014 || Belfon, Kellon || PhD CHE || Simmerling || Rizzo || Raleigh<br />
|-<br />
| 2015-2014 || Cortes, Michael || PhD AMS || Rizzo || Balazsi || Green<br />
|-<br />
| 2015-2014 || Elkin, Rena || PhD AMS || MacCarthy || Tannenbaum || Balazsi<br />
|-<br />
| 2015-2014 || Lee, Stella || PhD AMS || Levy || MacCarthy || Dill<br />
|-<br />
| 2015-2014 || Sam-Ang, Panu || PhD AMS || Balazsi || Green || Reuter<br />
|-<br />
| 2015-2014 || Santos, Ruda || PhD BSB || Green || Li || Rizzo<br />
|-<br />
| 2015-2014 || Hassan, Mosavverul || MS AMS || Seeliger || Coutsias || Simmerling<br />
|-<br />
| 2015-2014 || Yin, Xingyu || PhD BSB || Glyn || Rizzo || Garcia-Diaz<br />
<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2014-2013 || Kennedy, Chelsea || PhD AMS || Zhu || Rizzo || Green<br />
|-<br />
| 2014-2013 || Li, Fangfei || PhD AMS || Rizzo || Green || Coutsias<br />
|-<br />
| 2014-2013 || Yu, Bihua || PhD AMS || Green || Coutsias || Zhu<br />
|-<br />
| 2014-2013 || Zhou, Junjie || PhD CHE || Rizzo || Raleigh || Simmerling<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2013-2012 || Krantsevich, Artyom || PhD AMS || MacCarthy || Schatz || Green<br />
|-<br />
| 2013-2012 || Krantsevich, Nick || PhD AMS || Rizzo || MacCarthy || Schatz<br />
|-<br />
| 2013-2012 || Li, Xindy || PhD AMS || Rizzo || Green || MacCarthy<br />
|-<br />
| 2013-2012 || Yuan, Chaohui || PhD AMS || MacCarthy || Rizzo || Green<br />
|-<br />
| 2013-2012 || Guo, Jiaye || PhD BSB || Boon || Rizzo || -<br />
|-<br />
| 2013-2012 || Shan, Emma || MS AMS || - || MacCarthy || -<br />
|-<br />
| 2013-2012 || Chen, Ye || MS AMS || - || - || MacCarthy<br />
|-<br />
| 2013-2012 || Amgalan, Anar || PhD PHY || Dill || Rizzo || Maslov<br />
|- style="background:lightblue"<br />
| || || || || ||<br />
|-<br />
| 2012-2011 || Jeewon, Sin || PhD AMS || Rizzo || Green || MacCarthy<br />
|-<br />
| 2012-2011 || Chen, Jeff || PhD AMS || Schatz || Maslov || MacCarthy<br />
|-<br />
| 2012-2011 || Sinayev, Roman || AMS MS || Green || Rizzo || Simmerling<br />
|-<br />
| 2012-2011 || Xia, Yunting || AMS MS || Rizzo || MacCarthy || Green<br />
|-<br />
| 2012-2011 || Zhou, Yuchen || AMS MS || Green || Rizzo || MacCarthy<br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, "disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=151192022-2023 AMS-532 Fall-Spring2022-10-21T14:36:29Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || Liu et al; Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. ''Frontiers in Genetics'' '''2021''', ''12'', Article 655536<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || Watson et al; The evolutionary dynamics and fitness landscape of clonal hematopoiesis. ''Science'' '''2020''', ''367'', 1449<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || Smaers et al; Brain size expansion in primates and humans is explained by a selective modular expansion of the cortico-cerebellar system. ''Cortex'' '''2019''', ''118'', 292-305<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || Wiegand et al; Consequences of spatial patterns for coexistence in species-rich plant communities. ''Nature Ecology & Evolution'' '''2021''', ''5'', 965-973<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || Strey; Estimation of parameters from time traces originating from an Ornstein-Uhlenbeck process. ''PHYSICAL REVIEW E'' '''2019''', ''100'', -62142<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=151022022-2023 AMS-532 Fall-Spring2022-09-14T13:53:25Z<p>Rizzo: /* Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage */</p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=151012022-2023 AMS-532 Fall-Spring2022-09-14T13:53:03Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes:<br />
<br />
(i) What was the primary purpose of the study ?<br />
(ii) What aspects of the study do you feel was particularly well described or was compelling ?<br />
(iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=151002022-2023 AMS-532 Fall-Spring2022-09-14T13:51:52Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. Only in emergencies, if a class participant is unable to come to class, they can submit a 1-page max paper summary that includes:<br />
<br />
(1) What was the primary purpose of the study ?<br />
(2) What aspects of the study do you feel was particularly well described or was compelling ?<br />
(3) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150992022-2023 AMS-532 Fall-Spring2022-09-14T13:51:43Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. All students must attend each class but if for some reason they cannot attend a particular class due to unforeseen circumstances they must submit 1-page max summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150982022-2023 AMS-532 Fall-Spring2022-09-14T13:48:53Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. Only in emergencies, if a class participant is unable to come to class, they can submit a 1-page max paper summary that includes:<br />
<br />
(1) What was the primary purpose of the study ?<br />
(2) What aspects of the study do you feel was particularly well described or was compelling ?<br />
(3) What aspects of the study do you feel needs improvement ?<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150972022-2023 AMS-532 Fall-Spring2022-09-12T15:15:42Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || Nadeem et al; Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation. ''arXiv:2006.14566''<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150962022-2023 AMS-532 Fall-Spring2022-09-12T15:10:43Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || Delamonica, Brenda || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.14 Wed || Grange, Daniel || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.21 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.09.28 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.05 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.12 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45<br />
|-<br />
<br />
| 2022.10.19 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Last, First || -- || -- || TBD<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150932022-2023 AMS-532 Fall-Spring2022-08-31T17:12:10Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2022 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || -- || -- || -- || Organizational Meeting<br />
|-<br />
<br />
| 2022.09.14 Wed || Delamonica, Brenda || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.21 Wed || Grange, Daniel || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.28 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.05 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.12 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.19 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150922022-2023 AMS-532 Fall-Spring2022-08-31T17:11:11Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2021 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || -- || -- || -- || Organizational Meeting<br />
|-<br />
<br />
| 2022.09.14 Wed || Delamonica, Brenda || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.21 Wed || Grange, Daniel || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.28 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.05 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.12 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.19 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Cheung, Andrew || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=AMS-535_Introduction_to_Computational_Structural_Biology_and_Drug_Design&diff=15084AMS-535 Introduction to Computational Structural Biology and Drug Design2022-08-28T21:35:55Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu]<br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on class discussion/attendance, oral presentations, and quizzes.<br />
<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php<br />
<br />
<br />
<br />
== Course Schedules==<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2004_AMS535_Fall/course_syllabus.htm 2004 AMS-535 Fall]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2005_AMS535_Fall/course_syllabus.htm 2005 AMS-535 Fall]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2006_AMS535_Fall/course_syllabus.htm 2006 AMS-535 Fall]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2007_AMS535_Fall/course_syllabus.htm 2007 AMS-535 Fall]<br />
*[[2008 AMS-535 Fall]]<br />
*[[2009 AMS-535 Fall]]<br />
*[[2010 AMS-535 Fall]]<br />
*[[2011 AMS-535 Fall]]<br />
*[[2012 AMS-535 Fall]]<br />
*[[2013 AMS-535 Fall]]<br />
*[[2014 AMS-535 Fall]]<br />
*[[2015 AMS-535 Fall]]<br />
*[[2016 AMS-535 Fall]]<br />
*[[2017 AMS-535 Fall]]<br />
*[[2018 AMS-535 Fall]]<br />
*[[2019 AMS-535 Fall]]<br />
*[[2020 AMS-535 Fall]]<br />
*[[2021 AMS-535 Fall]]<br />
*[[2022 AMS-535 Fall]]</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=150832022 AMS-535 Fall2022-08-28T21:35:29Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || ESS 069, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
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<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Last, First mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
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| <center>2022.10.05 Wed </center><br />
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*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
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| <center>2022.10.10 Mon</center><br />
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*''No Class: Fall Break''<br />
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| <center>2022.10.12 Wed</center><br />
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*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
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| <center>2022.10.17 Mon</center><br />
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*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Last, First mp4 ]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Last, First mp4 ]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
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||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
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|-<br />
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| <center>2022.10.19 Wed </center><br />
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'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
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|-<br />
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| <center>2022.10.24 Mon</center><br />
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*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Last, First mp4] <br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
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1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
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| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
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<br />
| <center>2022.10.31 Mon</center><br />
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*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
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| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
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|-<br />
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| <center>2022.11.07 Mon</center><br />
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*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
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|- style="background:lightgreen"<br />
| <center>-</center><br />
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||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
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<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Last, FIrst mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=AMS-535_Introduction_to_Computational_Structural_Biology_and_Drug_Design&diff=15082AMS-535 Introduction to Computational Structural Biology and Drug Design2022-08-28T21:34:59Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu]<br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || Online, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on class discussion/attendance, oral presentations, and quizzes.<br />
<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php<br />
<br />
<br />
<br />
== Course Schedules==<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2004_AMS535_Fall/course_syllabus.htm 2004 AMS-535 Fall]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2005_AMS535_Fall/course_syllabus.htm 2005 AMS-535 Fall]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2006_AMS535_Fall/course_syllabus.htm 2006 AMS-535 Fall]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2007_AMS535_Fall/course_syllabus.htm 2007 AMS-535 Fall]<br />
*[[2008 AMS-535 Fall]]<br />
*[[2009 AMS-535 Fall]]<br />
*[[2010 AMS-535 Fall]]<br />
*[[2011 AMS-535 Fall]]<br />
*[[2012 AMS-535 Fall]]<br />
*[[2013 AMS-535 Fall]]<br />
*[[2014 AMS-535 Fall]]<br />
*[[2015 AMS-535 Fall]]<br />
*[[2016 AMS-535 Fall]]<br />
*[[2017 AMS-535 Fall]]<br />
*[[2018 AMS-535 Fall]]<br />
*[[2019 AMS-535 Fall]]<br />
*[[2020 AMS-535 Fall]]<br />
*[[2021 AMS-535 Fall]]<br />
*[[2022 AMS-535 Fall]]</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=150812022 AMS-535 Fall2022-08-28T21:34:27Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || Laufer Center Lecture Hall, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>in class lecture</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Last, First mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
<br />
| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
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| <center>2022.10.10 Mon</center><br />
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*''No Class: Fall Break''<br />
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| <center>2022.10.12 Wed</center><br />
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*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
|-<br />
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| <center>2022.10.17 Mon</center><br />
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*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Last, First mp4 ]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Last, First mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
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|- style="background:lightgreen"<br />
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||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
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|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
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*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Last, First mp4] <br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
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||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
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<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
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*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
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| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
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|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
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|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
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|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Last, FIrst mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150802022-2023 AMS-532 Fall-Spring2022-08-24T17:58:45Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2021 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || -- || -- || -- || Organizational Meeting<br />
|-<br />
<br />
| 2022.09.14 Wed || Delamonica, Brenda || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.21 Wed || Grange, Daniel || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.28 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.05 Wed || Song, Joon-Hyun || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.12 Wed || Chowdhury, Nabil || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.19 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Li, Stan || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Moy, Olivia || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Cheung, Andrewl || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2023.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2023.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2023.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2023.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2023.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2023.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2023.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2023.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2023.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2023.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2023.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2023.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150792022-2023 AMS-532 Fall-Spring2022-08-24T17:33:19Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2021 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2022.08.24 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.08.31 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2022.09.07 Wed || -- || -- || -- || Organizational Meeting<br />
|-<br />
<br />
| 2022.09.14 Wed || Delamonica, Brenda || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.21 Wed || Grange, Daniel || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.09.28 Wed || Rajesh, Chandana || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.05 Wed || Grange, Daniel || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.12 Wed || -- || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.19 Wed || Dean, Noah || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.10.26 Wed || Feltman, Scott || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.02 Wed || Joon-Hyun, Song || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.09 Wed || Carter, Simon || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.16 Wed || Huffstutler, Thomas || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
<br />
| 2022.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2022.11.30 Wed || Chowdury, Nabil|| -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2023.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2022.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2022.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2022.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2022.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2022.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2022.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2022.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2022.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2022.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2022.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2022.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2022.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2022.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2022.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022-2023_AMS-532_Fall-Spring&diff=150782022-2023 AMS-532 Fall-Spring2022-08-24T15:28:31Z<p>Rizzo: Created page with "=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === <br> {| align="center" border="2" cellpadding="8" cellspacing="0" style="back..."</p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 11:45PM - 12:40PM, Melville Library E4315<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br><br />
<br />
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==<br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:lightblue"<br />
| '''2021 Fall<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''References<br />
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''<br />
|-<br />
<br />
| 2021.08.25 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2021.09.01 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).<br />
|-<br />
<br />
| 2021.09.08 Wed || -- || -- || -- || First regular day of Journal Club. Dima Kozakov research presentation.<br />
|-<br />
<br />
| 2021.09.15 Wed ||-- || -- || -- || Organizational Meeting<br />
|-<br />
<br />
| 2021.09.22 Wed || Hall, Carole || -- || -- || McDowall et al; Ultra-Fine Scale Spatially-Integrated Mapping of Habitat and Occupancy Using Structure- From-Motion. ''PLOSone'' '''2017''', DOI:10.1371/journal.pone.0166773<br />
|-<br />
<br />
| 2021.09.29 Wed || Rajesh, Chandana || -- || -- || Kelley et al; Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. ''Genome Research'' '''2016''', ''26'', 990-999.<br />
|-<br />
<br />
| 2021.10.06 Wed || Grange, Daniel || -- || -- || Shiebinger et al; Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. ''Cell'' '''2019''', ''176'', 928-943. <br />
|-<br />
<br />
| 2021.10.13 Wed || -- || -- || -- || IACS Meet & Greet<br />
|-<br />
<br />
| 2021.10.20 Wed || Dean, Noah || -- || -- || Kumar et al; Ground-truth “resting-state” signal provides data-driven estimation and correction for scanner distortion of fMRI time-series dynamics. ''NeuroImage'' '''2021''', ''227'', 117584<br />
|-<br />
<br />
| 2021.10.27 Wed || Feltman, Scott || -- || -- || Krzysztoń et al; Single-cell kinetics of siRNA-mediated mRNA degradation. ''Nanomedicine: Nanotechnology, Biology, and Medicine'' '''2019''', ''21'', 102077.<br />
|-<br />
<br />
| 2021.11.03 Wed || Joon-Hyun, Song || -- || -- || Ghani et al; Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro. bioRxiv preprint doi: https://doi.org/10.1101/2021.09.07.459290<br />
|-<br />
<br />
| 2021.11.10 Wed || Carter, Simon and Foran, Chris || -- || -- || La Camera et al; Cortical computations via metastable activity. ''Current Opinion in Neurobiology'' '''2019''', ''58'', 37-45.<br> Perez et al; Accelerating physical simulations of proteins by leveraging external knowledge. ''Comput Mol Sci'' '''2017''', ''e1309''<br />
|-<br />
<br />
| 2021.11.17 Wed || Huffstutler, Thomas and Delamonica, Brenda || -- || -- || Koo et al; Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms. ''Current Opinion in Systems Biology'' '''2020''', ''19'', 16-23.<br> Bintu et al; Transcriptional regulation by the numbers: models. ''Curr Opin Genet Dev'' '''2005''', ''15'', 116-24.<br />
|-<br />
<br />
| 2021.11.24 Wed || -- || -- || -- || THANKSGIVING BREAK<br />
|-<br />
<br />
| 2021.12.01 Wed || Jiang, Yuhe and Chowdury, Nabil|| -- || -- || Jeronimo et al; FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. ''Molecular Cell'' '''2021''', ''81'', 3542–3559. <br> Emms et al; OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. ''Genome Biology'' '''2015''', ''16'', 157.<br />
|-<br />
|- style="background:lightgreen"<br />
| '''2022 Spring'''<br />
| '''Participant''' <br />
| '''Rotations or Research Group'''<br />
| '''Topic'''<br />
| '''NOTE: This semester (Spring 2022) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:'''<br />
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500<br />
|-<br />
| 2022.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||<br />
<br />
Discussion of Overall Course Requirements which include: <br />
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]<br />
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org<br />
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics<br />
|-<br />
<br />
| 2022.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]<br />
<br />
<br />
Readings (Nature articles)<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]<br />
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]<br />
<br />
<br />
Discussion<br />
*Why is the class important?<br />
*How should we behave as scientists?<br />
*How is science a social enterprise?<br />
|-<br />
<br />
| 2022.02.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]<br />
<br />
<br />
Reading <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?<br />
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?<br />
*Why do people commit scientific misconduct?<br />
*What are some consequences of committing scientific misconduct?<br />
*Who are some of your mentors?<br />
|-<br />
<br />
| 2022.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || <br />
Stony Brook Lecture<br />
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]<br />
<br />
<br />
Discussion<br />
*What qualities do you want in a mentor?<br />
*What are the challenges associated with being a mentor?<br />
*What does Professor Rubin mean when he says it is very important not to burn bridges?<br />
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?<br />
|-<br />
<br />
| 2022.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]<br />
<br />
<br />
Discussion (also from the above Columbia course)<br />
*Is it ever appropriate for authorship to change during a project or potential paper?<br />
*How should authorship roles be defined?<br />
*What are some abuses of authorship?<br />
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?<br />
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?<br />
*Why are acknowledgments so important?<br />
|-<br />
<br />
| 2022.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]<br />
<br />
<br />
Readings <br />
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]<br />
<br />
<br />
Discussion<br />
*Is plagiarism really that bad?<br />
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?<br />
|-<br />
<br />
| 2022.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]<br />
<br />
<br />
Readings <br />
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?<br />
*From Case Study 2: Under what condition is copying allowed?<br />
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.<br />
*How many years past a publication, if asked, should a researcher be able provide "raw data"? <br />
|-<br />
| 2022.03.16 Wed || -- || -- || -- || SPRING BREAK<br />
|-<br />
| 2022.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]<br />
<br />
<br />
Readings (3 Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]<br />
<br />
<br />
Discussion<br />
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?<br />
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?<br />
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy? <br />
|-<br />
<br />
| 2022.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]<br />
<br />
<br />
Readings: (Background Information, Case Studies, Helsinki Manuscript)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]<br />
<br />
Discussion<br />
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?<br />
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?<br />
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?<br />
|-<br />
<br />
| 2022.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||<br />
Stony Brook Lecture<br />
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]<br />
<br />
<br />
Readings (Case Studies)<br />
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]<br />
<br />
<br />
<br />
Discussion<br />
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?<br />
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?<br />
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?<br />
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?<br />
*What are some advantages of using Animals in experiments?<br />
*Discuss the three R's?<br />
*Is our class for or against Animal testing?<br />
|-<br />
| 2022.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2022.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2022.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
| 2022.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS<br />
|-<br />
<br />
|}<br />
<br />
<br><br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=AMS-532_Journal_Club_in_Computational_Biology&diff=15077AMS-532 Journal Club in Computational Biology2022-08-24T15:27:24Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || Wed 12:00PM - 12:53PM, Melville Library E4315<br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php<br />
<br />
== Course Schedules==<br />
<br />
*[[2006-2007 AMS-532 Fall-Spring]]<br />
<br />
*[[2007-2008 AMS-532 Fall-Spring]]<br />
<br />
*[[2008-2009 AMS-532 Fall-Spring]]<br />
<br />
*[[2009-2010 AMS-532 Fall-Spring]]<br />
<br />
*[[2010-2011 AMS-532 Fall-Spring]]<br />
<br />
*[[2011-2012 AMS-532 Fall-Spring]]<br />
<br />
*[[2012-2013 AMS-532 Fall-Spring]]<br />
<br />
*[[2013-2014 AMS-532 Fall-Spring]]<br />
<br />
*[[2014-2015 AMS-532 Fall-Spring]]<br />
<br />
*[[2015-2016 AMS-532 Fall-Spring]]<br />
<br />
*[[2016-2017 AMS-532 Fall-Spring]]<br />
<br />
*[[2017-2018 AMS-532 Fall-Spring]]<br />
<br />
*[[2018-2019 AMS-532 Fall-Spring]]<br />
<br />
*[[2019-2020 AMS-532 Fall-Spring]]<br />
<br />
*[[2020-2021 AMS-532 Fall-Spring]]<br />
<br />
*[[2021-2022 AMS-532 Fall-Spring]]<br />
<br />
*[[2022-2023 AMS-532 Fall-Spring]]</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=AMS-532_Journal_Club_in_Computational_Biology&diff=15076AMS-532 Journal Club in Computational Biology2022-08-24T15:26:13Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
|Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]<br />
|-<br />
| '''Course No.''' || AMS-532 <br />
|-<br />
| '''Location/Time''' || ONLINE, Wed 11:45PM - 12:40PM <br />
|-<br />
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.<br />
<br />
'''Learning Objectives:'''<br />
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. <br />
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). <br />
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).<br />
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: <br />
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training<br />
**(ii) Integrity in Scholarship<br />
**(iii) Scientific Misconduct<br />
**(iv) Mentoring<br />
**(v) Ownership and Authorship<br />
**(vi) Plagiarism<br />
**(vii) Data Management<br />
**(viii) Journalism and Science<br />
**(ix) Responsible Conduct of Research Involving Human Subjects<br />
**(x) Responsible Conduct of Research Involving Laboratory Animals<br />
<br />
<br />
<br />
'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.<br />
<br />
<br />
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings. <br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
<br />
<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php<br />
<br />
== Course Schedules==<br />
<br />
*[[2006-2007 AMS-532 Fall-Spring]]<br />
<br />
*[[2007-2008 AMS-532 Fall-Spring]]<br />
<br />
*[[2008-2009 AMS-532 Fall-Spring]]<br />
<br />
*[[2009-2010 AMS-532 Fall-Spring]]<br />
<br />
*[[2010-2011 AMS-532 Fall-Spring]]<br />
<br />
*[[2011-2012 AMS-532 Fall-Spring]]<br />
<br />
*[[2012-2013 AMS-532 Fall-Spring]]<br />
<br />
*[[2013-2014 AMS-532 Fall-Spring]]<br />
<br />
*[[2014-2015 AMS-532 Fall-Spring]]<br />
<br />
*[[2015-2016 AMS-532 Fall-Spring]]<br />
<br />
*[[2016-2017 AMS-532 Fall-Spring]]<br />
<br />
*[[2017-2018 AMS-532 Fall-Spring]]<br />
<br />
*[[2018-2019 AMS-532 Fall-Spring]]<br />
<br />
*[[2019-2020 AMS-532 Fall-Spring]]<br />
<br />
*[[2020-2021 AMS-532 Fall-Spring]]<br />
<br />
*[[2021-2022 AMS-532 Fall-Spring]]<br />
<br />
*[[2022-2023 AMS-532 Fall-Spring]]</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=150712022 AMS-535 Fall2022-08-18T14:59:14Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || Laufer Center Lecture Hall, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to completed each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.23.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
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| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
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| <center>2022.09.21 Wed </center><br />
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*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Last, First mp4] <br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
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||<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
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<center>-</center><br />
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| <center>2022.09.26 Mon</center><br />
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*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
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<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
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<center>-</center><br />
|-<br />
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|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
|-<br />
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| <center>2022.10.03 Mon </center><br />
|| <br />
*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
|-<br />
<br />
| <center>2022.10.05 Wed </center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
|-<br />
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|- style="background:peachpuff"<br />
| <center>2022.10.10 Mon</center><br />
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*''No Class: Fall Break''<br />
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<br />
| <center>2022.10.12 Wed</center><br />
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*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
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||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
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| <center>2022.10.17 Mon</center><br />
|| <br />
*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Last, First mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf pdf]<br />
<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Last, First mp4 ]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
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|-<br />
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|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.10.19 Wed </center><br />
||<br />
'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
<br />
|-<br />
<br />
| <center>2022.10.24 Mon</center><br />
||<br />
*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Last, First mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf pdf] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
<br />
||<br />
<br />
1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
|-<br />
<br />
| <center>2022.10.26 Wed</center><br />
|| <br />
*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
|-<br />
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<center>-</center><br />
|-<br />
<br />
| <center>2022.10.31 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.11.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
|-<br />
<br />
| <center>2022.11.02 Wed</center><br />
||<br />
*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
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|-<br />
<br />
| <center>2022.11.07 Mon</center><br />
|| <br />
*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]<br />
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|-<br />
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|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.09 Wed</center><br />
||<br />
'''SECTION V: LEAD REFINEMENT<br />
*''Free Energy Methods''<br />
:1. Thermolysin with two ligands (FEP)<br />
:2. Fatty acid synthase I ligands (TI)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]<br />
<br />
||<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]<br />
<br />
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]<br />
|-<br />
<br />
| <center>2022.11.14 Mon</center><br />
|| <br />
<br />
*'' MM-PB/GBSA''<br />
:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods<br />
*''MM-GBSA case studies''<br />
:2. EGFR and mutants<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]<br />
||<br />
<br />
|-<br />
<br />
| <center>2022.11.16 Wed </center><br />
|| <br />
*''MM-GBSA case studies''<br />
:1. ErbB family selectivity <br />
*''Linear Response'' <br />
:2. Intro to Linear Response (LR method) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.pdf pdf]<br />
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||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]<br />
<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.11.21 Mon </center><br />
|| <br />
*''Linear Response'' <br />
:1. Inhibition of protein kinases (Extended LR method) <br />
*''Properties of Known Drugs''<br />
:2. Molecular Scaffolds (frameworks) and functionality (side-chains<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]<br />
<br />
||<center>-</center><br />
|-<br />
|- style="background:peachpuff"<br />
| <center>2021.11.23 Wed</center><br />
|| <br />
*''No Class: Thanksgiving''<br />
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|-<br />
<br />
| <center>2022.11.28 Mon </center><br />
||<br />
*''Properties of Known Drugs''<br />
:1. Lipinski Rule of Five<br />
:2 ADME Prediction<br />
|| <br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]<br />
|-<br />
|-<br />
<br />
| <center>2022.11.30 Wed </center><br />
|| <br />
*''Properties of Known Drugs''<br />
:1. Synthetic Accessibility<br />
:2. QED<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4 Last, FIrst mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]<br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.12.05 Mon </center><br />
|| <br />
*''From Target to Market''<br />
:1. Drug Discovery Overview<br />
:2. Attrition Rates<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk02.pdf pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.; et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]<br />
||<center><br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]<br />
</center><br />
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|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
|<center>-</center><br />
||<br />
*'''''Final Exam''''' <br />
||<center>-</center><br />
||No Final Exam in AMS-535/CHE-535 for Fall 2022<br />
||<center>-</center><br />
|-<br />
|}<br />
<br />
== '''Required Syllabi Statements:''' ==<br />
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php<br />
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<br />
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.<br />
<br />
<br />
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html<br />
<br />
<br />
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php</div>Rizzohttps://ringo.ams.stonybrook.edu/index.php?title=2022_AMS-535_Fall&diff=150702022 AMS-535 Fall2022-08-18T14:53:10Z<p>Rizzo: </p>
<hr />
<div>=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===<br />
<br><br />
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"<br />
|- style="background:white"<br />
! style="width:10%" | '''Instructor''' <br />
| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]<br />
<br />
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] <br />
|-<br />
| '''Course No.''' || AMS-535 / CHE-535<br />
|-<br />
| '''Location/Time''' || Laufer Center Lecture Hall, Monday and Wednesday 2:40PM - 4:00PM<br />
|-<br />
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129<br />
|-<br />
| '''Grading''' || Grades will be based on the quality of: <br><br />
<br />
(1) Pre-recorded oral presentations (25%)<br />
::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br><br />
(2) Class discussion (30%)<br />
::At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class <br><br />
(3) Take home quizzes (45%)<br />
::Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped<br />
|-<br />
|}<br />
<br><br />
'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.<br />
<br />
<br />
'''Learning Objectives'''<br />
*(1) Become informed about the field of computational structure-based drug design and the pros and cons. <br />
*(2) Dissect seminal theory and application papers relevant to computational drug design. <br />
*(3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design. <br />
*(4) Read, participate in discussion, and be tested across five key subject areas:<br />
**(i) Drug Discovery and Biomolecular Structure: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure<br />
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics), <br />Solvent Models, Condensed-phase Calculations, Parameter Development<br />
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding<br />
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications<br />
**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction<br />
<br />
<br />
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.<br />
<br />
<br />
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.<br />
<br />
== '''Syllabus Notes''' ==<br />
This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:<br />
<br />
'''General Information:'''<br />
*We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.<br />
*The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.<br />
*All class correspondence should be addressed to ALL course Instructors.<br />
<br />
'''Discussion Sessions:'''<br />
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class. <br />
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered. <br />
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to submit a one page [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.<br />
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. <br />
*Please note that this is an in-person class and all participants are expected to attend each and every class.<br />
<br />
'''Oral Presentations:'''<br />
*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below. <br />
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed. <br />
*Course participants will watch the student presentations before the class in which they are to be discussed.<br />
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.<br />
<br />
'''Take home Quizzes:'''<br />
*At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.<br />
*Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary. <br />
*Students will have 24 hours to completed each Quiz. Late Quizzes will not be accepted.<br />
*Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. <br />
<br />
'''Recording Your Oral Presentations Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:<br />
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )<br />
*Open the Zoom app<br />
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)<br />
*Share your screen<br />
*Open your paper presentation in PPT and put in presentation mode<br />
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)<br />
*Stop recording and quit the meeting <br />
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good<br />
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)<br />
*Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )<br />
<br />
'''Oral Presentation Guidelines:''' Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:<br />
<br />
*Introduction/Background (include biological relevance if applicable)<br />
*Specifics of the System or General Problem<br />
*Computational Methods (theory) and Details (system setup) being used<br />
*Results and Discussion (critical interpretation of results and any problems/challenges)<br />
*Conclusions/Future<br />
*Acknowledgments<br />
<br />
<br><br />
<br><br />
<br />
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"<br />
|- style="background:cornflowerblue"<br />
| <center>'''Date'''</center><br />
| <center>'''Topic'''</center><br />
| <center>'''Speaker and Presentation'''</center><br />
| <center>'''Primary Reference'''</center><br />
| <center>'''Secondary Reference'''</center><br />
|-<br />
<br />
| <center>2022.08.22 Mon</center><br />
|| <br />
*''Organizational Meeting<br />
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.23.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]<br />
|| Course introduction and format. Go over Syllabus. Course participant background and introductions.<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.24 Wed</center><br />
||<br />
'''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''<br />
*''Drug Discovery''<br />
:1. Introduction, history, irrational vs. rational<br />
:2. Viral Target Examples<br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]<br />
||<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]<br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.29 Mon</center><br />
|| <br />
*''Chemistry Review''<br />
:1. Molecular structure, bonding, graphical representations <br />
:2. Functionality, properties of organic molecules <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.08.31 Wed</center><br />
|| <br />
*''Biomolecular Structure''<br />
:1. Lipids, carbohydrates <br />
:2. Nucleic acids, proteins <br />
<br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]<br />
|-<br />
<br />
|- style="background:peachpuff"<br />
| <center>2022.09.05 Mon</center><br />
|| <br />
*''No Class: Labor Day''<br />
||<center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.07 Wed</center><br />
|| <br />
*''Molecular Interactions and Recognition''<br />
:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)<br />
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| <center>-</center><br />
|-<br />
<br />
| <center>2022.09.12 Mon</center><br />
|| <br />
*''Intro. to Methods in 3-D Structure Determination''<br />
:1. Crystallography, NMR <br />
:2. Structure Quality, PDB in detail <br />
||<br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]<br />
<br><br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]<br />
|| <center>presentation</center><br />
|| <center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>-</center><br />
|-<br />
<br />
| <center>2022.09.14 Wed </center><br />
||<br />
'''SECTION II: MOLECULAR MODELING'''<br />
*''Classical Force Fields''<br />
:1. All-atom Molecular Mechanics<br />
:2. OPLS <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]<br />
|-<br />
<br />
| <center>2022.09.19 Mon</center><br />
|| <br />
*''Classical Force Fields''<br />
:1. AMBER<br />
*''Explicit Solvent Models''<br />
:2. Water models (TIP3P, TIP4P, SPC) <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]<br />
|-<br />
<br />
| <center>2022.09.21 Wed </center><br />
|| <br />
*''Explicit Solvent Models''<br />
:1. Condensed-phase calculations (DGhydration)<br />
*''Continuum Solvent Models''<br />
:2. Generalized Born Surface Area (GBSA)<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4 Last, First mp4] <br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf pdf]<br />
<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]<br />
<br />
<center>-</center><br />
|-<br />
<br />
| <center>2022.09.26 Mon</center><br />
|| <br />
*''Continuum Solvent Models''<br />
:1. Poisson-Boltzmann Surface Area (PBSA) <br />
:2. Accuracy of partial atomic changes for GBSA and PBSA <br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf pdf]<br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4 Last, First mp4]<br />
<br><br />
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf pdf]<br />
||<br />
<br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988] <br />
<br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]<br />
||<br />
<center>-</center><br />
|-<br />
<br />
|- style="background:lightgreen"<br />
| <center>-</center><br />
||<center>-</center><br />
||<center>-</center><br />
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
||<center>'''Additional resources:'''</center><br />
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br> <br />
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]<br />
|-<br />
<br />
| <center>2022.09.28 Wed </center><br />
||<br />
'''SECTION III: SAMPLING METHODS'''<br />
*''Molecular Conformations''<br />
:1. Small molecules, peptides, relative energy, minimization methods<br />
*''Sampling Methods for Large Simulations''<br />
:2. Molecular dynamics (MD) <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]<br />
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| <center>2022.10.03 Mon </center><br />
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*''Sampling Methods for Large Simulations''<br />
:1. Monte Carlo (MC)<br />
*''Predicting Protein Structure'' <br />
:2. Ab initio structure prediction (protein-folding) <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]<br />
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| <center>2022.10.05 Wed </center><br />
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*''Predicting Protein Structure''<br />
:1. Example Trp-cage<br />
:2. Comparative (homology) modeling <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]<br />
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| <center>2022.10.10 Mon</center><br />
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*''No Class: Fall Break''<br />
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| <center>2022.10.12 Wed</center><br />
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*''Predicting Protein Structure'' <br />
:1. Case studies (CASP)<br />
:2. Accelerated MD for Blind Protein Prediction <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk01.pdf pdf]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.pdf pdf]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]<br />
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| <center>2022.10.17 Mon</center><br />
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*''Predicting Protein Structure''<br />
:1. Meso-Scale MD (Markov State Models) <br />
:2. Neural Networks<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Last, First mp4 ]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Last, First mp4 ]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf pdf ]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]<br />
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||<center>'''Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center><br />
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| <center>2022.10.19 Wed </center><br />
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'''SECTION IV: LEAD DISCOVERY'''<br />
*''Docking''<br />
:1. Introduction to DOCK<br />
:2. Test Sets (database enrichment) <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Last, First mp4]<br />
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.pdf pdf]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]<br />
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| <center>2022.10.24 Mon</center><br />
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*''Docking'' <br />
:1. Test Sets (virtual screening)<br />
:2. Footprint-based scoring<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Last, First mp4] <br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]<br />
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1. [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]<br />
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| <center>2022.10.26 Wed</center><br />
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*''Docking''<br />
:1. GIST score<br />
*''Discovery Methods'' <br />
:2. Hotspot probes (GRID) <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]<br />
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| <center>2022.10.31 Mon</center><br />
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*''Discovery Methods'' <br />
:1. COMFA<br />
:2 Pharmacophores<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]<br />
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| <center>2022.11.02 Wed</center><br />
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*''Discovery Methods.'' <br />
:1. Pharmacophores<br />
:2. De novo design <br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Last, First mp4]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]<br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]<br />
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| <center>2022.11.07 Mon</center><br />
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*''Discovery Methods'' <br />
:1. De novo design<br />
:2. Genetic Algorithm <br />
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Last, First mp4]<br />
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1. [http://ringo.ams.sunysb.edu/~rizzo