Difference between revisions of "AMS-536 Molecular Modeling of Biological Molecules"

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(Please see http://rizzo.ams.sunysb.edu/ for Rizzo Group Homepage (Research and Teaching))
 
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=== <center> Please see http://rizzo.ams.sunysb.edu/ for Rizzo Group Homepage (Research and Teaching) </center> ===
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=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching) </center> ===
 
<br>
 
<br>
 
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
 
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
 
|- style="background:white"
 
|- style="background:white"
! style="width:10%" | '''Instructor'''
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|- style="background:white" ! style="width:10%"  
| Dr. William J. Allen  [631-632-8519, william.allen@stonybrook.edu]
 
  Dr. Robert C. Rizzo    [631-632-8519, rizzorc@gmail.com]
 
 
|-
 
|-
| '''Course No.''' || AMS-536
+
| '''Instructor''' || Dr. Robert C. Rizzo  [631-632-9340, robert dot rizzo -at- stonybrook.edu]
 
|-
 
|-
| '''Location/Time''' || Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:20PM - 3:40PM 
+
| '''Teaching Assistant''' || Steve Pak  [631-632-8519, steven dot pak - at - stonybrook dot edu]
 
|-
 
|-
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics
+
| '''Teaching Assistant''' || John Bickel  [631-632-8519, john dot bickel - at - stonybrook dot edu]
 +
|-
 +
| '''Course No.''' || AMS-536 / CHE-536
 +
|-
 +
| '''Location/Time''' || Online, Monday and Wednesday 2:40PM - 4:00PM
 +
|-
 +
| '''Office Hours''' || Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
 
|-
 
|-
 
| '''Acknowledgments''' || The AMS-536 instructors would like to thank: <br>
 
| '''Acknowledgments''' || The AMS-536 instructors would like to thank: <br>
 
(1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses <br>
 
(1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses <br>
(2) Yan Yu and the Seawulf team for cluster support <br>
+
(2) Firat Coskin and the entire IACS team for cluster support <br>
(3) Pat Tonra for Mathlab support
+
(3) Pat Tonra for Mathlab support <br>
 +
(4) Victor Poon for other computational support<br>
 
|-
 
|-
 
|}
 
|}
 
<br>
 
<br>
  
'''GENERAL INFORMATION:''' AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Familiarity with working in a Unix (Linux) environment is desirable.
+
'''GENERAL INFORMATION:''' AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Grades will be based on the quality of the talks, participation in class discussion, attendance, and the final written report. Familiarity with working in a Unix (Linux) environment is desirable.
 +
 
 +
 
 +
'''Learning Obectives:'''
 +
*(1) Gain hands-on experience modeling biological molecules at the atomic level. 
 +
*(2) Learn to navigate linx/unix operating system
 +
*(3) Learn shell scripting and text-based editing (vim program)
 +
*(4) Learn to use a linux-based computing cluster that has a queuing system
 +
*(5) Learn to use visualization software (Chimera, MOE, and VMD programs)
 +
*(6) Setup, execute, and analyze docking (DOCK) and molecular dynamics (AMBER) tutorials. 
 +
*(7) Give oral presentations on individual research projects which includes:
 +
**(i) Introduction/Background (include biological relevance)
 +
**(ii) Specifics of Your System
 +
**(iii) Computational Details (theory)
 +
**(iv) Computational Details (system setup)
 +
**(v) Results and Discussion (include a critical interpretation of your results)
 +
**(vi) Conclusions
 +
**(vii) Future
 +
**(viii) Acknowledgments
 +
*(8) Write a polished well-referenced manuscript in the format of a peer-reviewed Journal Article.
 +
 
  
  
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'''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.
 
'''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.
 
        
 
        
 +
== '''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
 +
  
'''REQUIRED SYLLABI STATEMENTS:''' The University Senate has authorized that the following required statements appear in all teaching syllabi on the Stony Brook Campus. This information is also located on the Provost’s website: http://www.stonybrook.edu/commcms/provost/policies.shtml
+
'''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.
  
  
'''Americans with Disabilities Act:''' If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Disability Support Services, ECC(Educational Communications Center) Building, Room 128, (631)632-6748. They will determine with you what accommodations, if any, are necessary and appropriate. All information and documentation is confidential.  https://web.stonybrook.edu/newfaculty/StudentResources/Pages/DisabilitySupportServices.aspx.  
+
'''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
  
  
'''Academic Integrity:''' 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/uaa/academicjudiciary/
+
'''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
  
  
'''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 school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.
 
  
 
== Course Schedules==
 
== Course Schedules==
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2005_AMS536_Spring/course_syllabus.htm 2005 AMS-536 Spring]
+
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2005_AMS536_Spring/course_syllabus.htm 2005 AMS-536 Spring]
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2006_AMS536_Spring/course_syllabus.htm 2006 AMS-536 Spring]
+
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2006_AMS536_Spring/course_syllabus.htm 2006 AMS-536 Spring]
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2007_AMS536_Spring/course_syllabus.htm 2007 AMS-536 Spring]
+
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2007_AMS536_Spring/course_syllabus.htm 2007 AMS-536 Spring]
 
*[[2008 AMS-536 Spring]]
 
*[[2008 AMS-536 Spring]]
 
*[[2009 AMS-536 Spring]]
 
*[[2009 AMS-536 Spring]]
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*[[2012 AMS-536 Spring]]
 
*[[2012 AMS-536 Spring]]
 
*[[2013 AMS-536 Spring]]
 
*[[2013 AMS-536 Spring]]
 +
*[[2014 AMS-536 Spring]]
 +
*[[2015 AMS-536 Spring]]
 +
*[[2016 AMS-536 Spring]]
 +
*[[2017 AMS-536 Spring]]
 +
*[[2018 AMS-536 Spring]]
 +
*[[2019 AMS-536 Spring]]
 +
*[[2020 AMS-536 Spring]]
 +
*[[2021 AMS-536 Spring]]
 +
*[[2022 AMS-536 Spring]]

Latest revision as of 15:05, 17 August 2021

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching)


Instructor Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]
Teaching Assistant Steve Pak [631-632-8519, steven dot pak - at - stonybrook dot edu]
Teaching Assistant John Bickel [631-632-8519, john dot bickel - at - stonybrook dot edu]
Course No. AMS-536 / CHE-536
Location/Time Online, Monday and Wednesday 2:40PM - 4:00PM
Office Hours Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
Acknowledgments The AMS-536 instructors would like to thank:

(1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses
(2) Firat Coskin and the entire IACS team for cluster support
(3) Pat Tonra for Mathlab support
(4) Victor Poon for other computational support


GENERAL INFORMATION: AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Grades will be based on the quality of the talks, participation in class discussion, attendance, and the final written report. Familiarity with working in a Unix (Linux) environment is desirable.


Learning Obectives:

  • (1) Gain hands-on experience modeling biological molecules at the atomic level.
  • (2) Learn to navigate linx/unix operating system
  • (3) Learn shell scripting and text-based editing (vim program)
  • (4) Learn to use a linux-based computing cluster that has a queuing system
  • (5) Learn to use visualization software (Chimera, MOE, and VMD programs)
  • (6) Setup, execute, and analyze docking (DOCK) and molecular dynamics (AMBER) tutorials.
  • (7) Give oral presentations on individual research projects which includes:
    • (i) Introduction/Background (include biological relevance)
    • (ii) Specifics of Your System
    • (iii) Computational Details (theory)
    • (iv) Computational Details (system setup)
    • (v) Results and Discussion (include a critical interpretation of your results)
    • (vi) Conclusions
    • (vii) Future
    • (viii) Acknowledgments
  • (8) Write a polished well-referenced manuscript in the format of a peer-reviewed Journal Article.


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.

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) 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.


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


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


Course Schedules