Difference between revisions of "2020 AMS535 Fall"
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:2. Accelerated MD for Blind Protein Prediction  :2. Accelerated MD for Blind Protein Prediction  
    
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<center></center>  <center></center>  
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Revision as of 11:35, 26 August 2020
Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage
Instructor  Dr. Robert C. Rizzo [6316328519, rizzorc at gmail.com]
Dr. Guilherme Duarte Ramos Matos [6316328519, guilherme dot duarteramosmatos at stonybrook dot edu] John Bickel [6316328519, john dot bickel at stonybrook dot edu] 

Course No.  AMS535 / CHE535 
Location/Time  Online, Monday and Wednesday 2:40PM  4:00PM 
Office Hours  Anytime by appointment, Math Tower 3129 
Grading  Grades will be based on the quality of: (1) Prerecorded oral presentations (25%)
(2) Class discussion (30%)
(3) Take home quizzes (45%)

GENERAL INFORMATION: AMS535 provides an introduction to the field of computational structurebased 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.
Learning Objectives
 (1) Become informed about the field of computational structurebased drug design and the pros and cons.
 (2) Dissect seminal theory and application papers relevant to computational drug design.
 (3) Gain practice in giving an indepth oral powerpoint presentation on computational drug design.
 (4) Read, participate in discussion, and be tested across five key subject areas:
 (i) Drug Discovery and Biomolecular Structure:
Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids
Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure  (ii) Molecular Modeling:
Classical Force Fields (Molecular Mechanics),
Solvent Models, Condensedphase Calculations, Parameter Development  (iii) Sampling Methods:
Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC)
Sampling Techniques, Predicting Protein Structure, Protein Folding  (iv) Lead Discovery:
Docking as a Lead Generation Tool, Docking Algorithms
Discovery Methods I, Discovery Methods II, Applications  (v) Lead Refinement:
Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)
MMPBSA, MMGBSA, Properties of Known Drugs, Property Prediction
 (i) Drug Discovery and Biomolecular Structure:
LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.
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.
Online Syllabus Notes
As a result of the COVID19 outbreak this course is being offered online. 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:
General Information:
 We will hold class at the regularly scheduled time (M/W 2:404:00PM) however this will be done online via ZOOM.
 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 and will be made available on the class website.
 All class correspondence should be addressed to ALL course Instructors.
Discussion Sessions:
 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 prerecorded videos made by students taking the class.
 During the Discussion sessions (ZOOM breakout rooms) the Instructors will ask participants to explain details of the papers they have read which will form the basis of the "Discussion" part of their grade. Thus, it is important that everyone attend all of the synchronous classes. All students are expected to participate especially those whose papers are being discussed that day. Breakout room discussion will NOT be recorded.
 If a student is unable to attend an online class they will instead be asked to submit a one page 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.
 If a students misses an online class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.
Oral Presentations:
 Students will prerecord 2 different ZOOM presentations based on 2 different papers from the schedule shown below.
 Students will email their prerecorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.
 Course participants will watch the student presentations before the class in which they are to be discussed.
 Course participants will score each student presentation using a Presentation Assessment Sheet which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.
Take home Quizzes:
 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.
 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.
 Students will have 24 hours to completed each Quiz. Late Quizzes will not be accepted.
 Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested.
Recording Your Oral Presentations Using Zoom: It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:
 Download the Zoom app ( https://it.stonybrook.edu/services/zoom )
 Open the Zoom app
 Create a new Zoom meeting with only yourself (make sure audio and video are turned on)
 Share your screen
 Open your paper presentation in PPT and put in presentation mode
 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)
 Stop recording and quit the meeting
 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
 Follow the above steps to create your "fulllength" video presentation (videos should not exceed 2025 minutes)
 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 )
Oral Presentation Guidelines: Prerecorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 2025 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:
 Introduction/Background (include biological relevance if applicable)
 Specifics of the System or General Problem
 Computational Methods (theory) and Details (system setup) being used
 Results and Discussion (critical interpretation of results and any problems/challenges)
 Conclusions/Future
 Acknowledgments







Rizzo, R. mp4  Course introduction and format. Go over Syllabus. Course participant background and introductions.  

SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE

1. Jorgensen, W.L., The many roles of computation in drug discovery. Science 2004, 303, 18138 2. Kuntz, I. D., Structurebased strategies for drug design and discovery. Science 1992, 257, 10781082 
 



 



structures of the 20 amino acid side chains  





Rizzo, R. mp4  



Rizzo, R. mp4  




SECTION II: MOLECULAR MODELING







 


 



SECTION III: SAMPLING METHODS

2. Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. Nature 1990, 347, 6319 



1. Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B. 2. Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4, 1019 













SECTION IV: LEAD DISCOVERY




2. Huang, N.; et al., Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49(23), 67896801 



 












SECTION V: LEAD REFINEMENT



















2. Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. J. Mol. Model, 2002, 8, 337349 










No Final Exam in AMS535/CHE535 for Fall 2020 
Required Syllabi Statements:
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
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) 6326748, 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/firesafety/emergencyevacuation/evacuationguidepeoplephysicaldisabilities and search Fire Safety and Evacuation and Disabilities.
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 schoolspecific 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
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 University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their schoolspecific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the FacultyEmployee Handbook.