View source for AMS-535 Introduction to Computational Structural Biology and Drug Design

=== <center> Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage </center> ===
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! style="width:10%" | '''Instructor''' 
| Dr. Robert C. Rizzo    [631-632-8519, rizzorc -at- gmail.com]

Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu]
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| '''Course No.''' || AMS-535  / CHE-535
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| '''Location/Time''' || FREY HALL 326 WESTCAMPUS, MoWe 2:00PM - 3:20PM
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| '''Office Hours''' || Anytime by appointment, Math Tower 3-129
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'''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.



'''Learning Objectives'''
*(1) Become informed about the field of computational structure-based 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 in-depth 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: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure
**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics),  <br />Solvent Models, Condensed-phase Calculations, Parameter Development
**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding
**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications
**(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


'''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==
*[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2004_AMS535_Fall/course_syllabus.htm 2004 AMS-535 Fall]
*[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2005_AMS535_Fall/course_syllabus.htm 2005 AMS-535 Fall]
*[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2006_AMS535_Fall/course_syllabus.htm 2006 AMS-535 Fall]
*[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2007_AMS535_Fall/course_syllabus.htm 2007 AMS-535 Fall]
*[[2008 AMS-535 Fall]]
*[[2009 AMS-535 Fall]]
*[[2010 AMS-535 Fall]]
*[[2011 AMS-535 Fall]]
*[[2012 AMS-535 Fall]]
*[[2013 AMS-535 Fall]]
*[[2014 AMS-535 Fall]]
*[[2015 AMS-535 Fall]]
*[[2016 AMS-535 Fall]]
*[[2017 AMS-535 Fall]]
*[[2018 AMS-535 Fall]]
*[[2019 AMS-535 Fall]]
*[[2020 AMS-535 Fall]]
*[[2021 AMS-535 Fall]]
*[[2022 AMS-535 Fall]]
*[[2023 AMS-535 Fall]]
*[[2024 AMS-535 Fall]]