2004 Fall Course Syllabus: AMS-535Introduction to Computational Structural Biology and Drug Design |
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Fall 2004 |
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, 2:20-3:40 PM, Room N3063, Library 3rd Floo |
Office Hours: | Tues/Fri, 2:00-4:00 PM or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
Note: | The original course number was AMS 691 section 2 |
Hyperlinks accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only. |
DRUG DISCOVERY / BIOMOLECULAR STRUCTURE (6 meetings) |
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Date |
Topics |
Speaker and Presentation |
Primary Reference |
Additional References |
2004.08.30 |
Organizational Meeting |
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2004.09.01 |
Drug Discovery
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and presentation |
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2004/09.08 |
Chemistry Review
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presentation |
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2004.09.13 |
Biomolecular Structure
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presentation |
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2004.09.15 |
Molecular Interactions and Recognition
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presentation |
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2004.09.20 | Experimental Techniques for Elucidating Structure
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R. Rizzo | presentation | |
MOLECULAR MODELING (5 meetings) |
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2004.09.22 |
All Atom Force Fields (Molecular Mechanics)
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2004.09.27 |
Explicit Solvent Models
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2004.09.29 |
Condensed Phase Calculations
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2004.10.04 |
Intro. to Thermodynamics
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2004.10.06 |
Intro. to Thermodynamics
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C. Simmerling (see above) |
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SAMPLING METHODS (5 meetings) |
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2004.10.11 |
Conformational Space
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2004.10.13 |
Molecular Dynamics (MD)
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2004.10.18 |
Metropolis Monte Carlo (MC)
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2004.10.20 |
Enhanced Sampling Techniques
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2004.10.25 | Predicting Protein Structure
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LEAD DISCOVERY (5 meetings) |
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2004.10.27 |
Docking I.
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2004.11.01 |
Docking II.
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2004.11.03 |
Discovery Methods I.
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2004.11.08 |
Discovery Methods II.
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2004.11.10 |
Discovery Methods Applications
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LEAD REFINEMENT (5 meetings) |
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2004.11.15 |
Binding Energy I. Free Energy Perturbation (FEP)
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2004.11.17 |
Binding Energy II. Linear Response
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R. Rizzo (chalk) |
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11.22.2004 |
Binding Energy III. MM-PBSA, MM-GBSA
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R. Rizzo (chalk) |
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2004.11.29 |
Properties of Known Drugs
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2004.12.01 |
Property Prediction
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MISCELLANEOUS (2 meetings) |
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2004.12.06 |
Nucleic Acid Stability
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2004.12.08 | Enhanced Sampling Revisited
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A. Okur | ||
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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. |