2006 Fall Course Syllabus: AMS-535
Introduction to Computational Structural Biology and Drug Design
Fall 2006
2006 Fall Course Syllabus: AMS-535Introduction to Computational Structural Biology and Drug Design |
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Fall 2006 |
| Instructor: | Dr. Robert C. Rizzo [631-632-9340, rizzo@ams.sunysb.edu] |
| Course: | AMS-535 (3 Credits / 0 Audit) http://www.ams.sunysb.edu/~rizzo (go to Teaching) |
| When: | Monday/Wednesday, 12:50-2:10 PM, ESS (Earth and Space Sciences) Room 079
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| Office Hours: | Anytime (call first) or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
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, and five quizzes. 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). |
| If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748. 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.ehs.sunysb.edu and search Fire Safety and Evacuation and Disabilities. |
| Hyperlinks accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only. |
Date |
Topics |
Speaker and Presentation |
Primary Reference |
Secondary |
2006.09.06 Wed |
Organizational Meeting |
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2006.09.11 Mon |
SECTION I: Drug Discovery
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presentation
and
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2006.09.13 Wed |
Chemistry Review
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presentation |
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2006.09.18 Mon |
Biomolecular Structure
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presentation |
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2006.09.20 Wed |
Molecular Interactions and Recognition
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presentation |
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2006.09.25 Mon |
Intro. to Methods in 3-D Structure Determination
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presentation |
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2006.09.27 Wed |
** Quiz Prior Section I ** SECTION II: Classical Force Fields
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2006.10.02 Mon | No Class (Yom Kippur) |
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2006.10.04 Wed |
Force Field Development
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2006.10.09 Mon |
Explicit Solvent Models
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2006.10.11 Wed |
Continuum Solvent Models
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2006.10.16 Mon | Guest Lecture: Sequence Alignment and Genomics
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Prof. Steve Skiena (guest lecture) |
presentation |
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2006.10.18 Wed |
** Quiz Prior Section II ** SECTION III: Molecular Conformation
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2006.10.23 Mon | Primary Sampling Methods for Computer Simultations
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2006.10.25 Wed | Predicting Protein Structure I.
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2006.10.30 Mon | Predicting Protein Structure II.
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2006.11.01 Wed | Enhanced Sampling Techniques
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2006.11.06 Mon |
** Quiz Prior Section III ** SECTION IV: Docking I.
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2006.11.08 Wed | Docking II.
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(guest lecture) |
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2006.11.13 Mon | Discovery Methods I.
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2006.11.15 Wed | Discovery Methods II.
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2006.11.20 Mon | Discovery Methods Applications
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2006.11.22 Wed |
** Quiz Prior Section IV ** SECTION V: Free Energy Perturbation (FEP)
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2006.11.27 Mon |
Linear Response
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2006.11.29 Wed |
MM-PBSA, MM-GBSA
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2006.12.04 Mon |
MM-PBSA, MM-GBSA.
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(guest lecture) |
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2006.12.06 Wed |
Guest Lecture
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Dr. Elizabeth Buck |
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2006.12.11 Mon |
Properties of Known Drugs
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2006.12.13 Wed | Property Prediction
** Quiz Prior Section V **
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