2007 Fall Course Syllabus: AMS-535Introduction to Computational Structural Biology and Drug Design |
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Fall 2007 |
Instructor: | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com]
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Course: | AMS-535 (3 Credits / 0 Audit) http://www.ams.sunysb.edu/~rizzo (go to Teaching) |
When: | Monday/Wednesday, 3:50-5:10 PM, Stony Brook Union, Room 237
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Office Hours: | Anytime (call first) or by appointment, Room 3-129, Dept. of Applied Math & Statistics |
COMPANION COURSE: A companion course taught in the Spring (AMS-536, "Molecular Modeling of Biological Molecules") gives hands-on experience in using computational methods discussed in the introductory Fall course. Students interested in taking the two-semester sequence should plan accordingly since AMS-535 (Fall) is a prerequisite for AMS-536 (Spring). |
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 myself, 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. Grades will be based on the quality of the talks, participation in class discussion, attendance, quizzes, and a final. |
DISABILITY SUPPORT SERVICES (DSS) STATEMENT: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748 or http://studentaffairs.stonybrook.edu/dss/ 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 Disability Support Services. For procedures and information go to the following website: http://www.stonybrook.edu/ehs/fire/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 are required to report any suspected instance of academic dishonesty to the Academic Judiciary. 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 Judicial Affairs any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, and/or inhibits students' ability to learn. |
LITERATURE: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only. |
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. |
EXAMPLE QUESTIONS FROM PREVIOUS EXAMS: 2007.ams535.example.questions.pdf |
Date |
Topics |
Speaker and Presentation |
Primary Reference |
Secondary |
2007.09.05 Wed |
Organizational Meeting |
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2007.09.10 Mon |
SECTION I: Drug Discovery
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Note: This presentation contain slides from a variety of online sources for educational and illustrative purposes only.
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2007.09.12 Wed |
Chemistry Review
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Note: This presentation contain slides from a variety of online sources for educational and illustrative purposes only. |
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2007.09.17 Mon |
Biomolecular Structure
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Note: This presentation contain slides from a variety of online sources for educational and illustrative purposes only. |
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2007.09.19 Wed |
Special Lecture ** NOTE ROOM CHANGE ** ** Chemistry Room 412 **
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Dr. Yuji Sugita |
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2007.09.24 Mon |
Molecular Interactions and Recognition
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Note: This presentation contain slides from a variety of online sources for educational and illustrative purposes only. |
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2007.09.26 Wed |
Intro. to Methods in 3-D Structure Determination
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Note: This presentation contain slides from a variety of online sources for educational and illustrative purposes only. |
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2007.10.01 Mon |
** Quiz Prior Section I ** SECTION II: Classical Force Fields
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2007.10.03 Wed |
Force Field Development
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2007.10.08 Mon |
Explicit Solvent Models
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2007.10.10 Wed |
Continuum Solvent Models
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2007.10.15 Mon |
** Quiz Prior Section II ** SECTION III: Molecular Conformation
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2007.10.17 Wed |
Primary Sampling Methods for Computer Simulations
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2007.10.22 Mon |
Predicting Protein Structure I.
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2007.10.24 Wed |
Predicting Protein Structure II.
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2007.10.29 Mon |
Enhanced Sampling Techniques
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2007.10.31 Wed |
** Quiz Prior Section III ** SECTION IV: Docking I.
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2007.11.05 Mon |
Docking II.
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2007.11.07 Wed |
Discovery Methods I.
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2007.11.12 Mon |
Discovery Methods II.
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2007.11.14 Wed |
Discovery Methods Applications
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2007.11.19 Mon |
SECTION V: Free Energy Perturbation (FEP)
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S. Mukherjee |
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2007.11.21 Wed |
No Class: University Correction Day |
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2007.11.26 Mon |
** Quiz Prior Section IV ** SECTION V cont: Linear Response
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2007.11.28 Wed |
MM-PBSA, MM-GBSA
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2007.12.03 Mon |
MM-GBSA
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Chan001.pdf | ||
2007.12.05 Wed |
Properties of Known Drugs
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2007.12.10 Mon |
Guest Lecture
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2007.12.12 Wed |
Review for Final Exam |
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2007.12.19 Wed |
** FINAL EXAM ** 5:00 - 7:30 PM |
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Unless otherwise noted the Final Exam will be given in our regular class room |