2005 Fall Course Syllabus: AMS-535Introduction to Computational Structural Biology and Drug Design |
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Fall 2005 |
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/Friday, 12:50-2:10 PM, Room N101, SOCBEHAV SCI |
Office Hours: | Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
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 |
08/29/2005 |
First class will meet on Friday |
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09/02/2005 |
Organizational Meeting |
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09/05/2005 | No class (labor day) |
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09/09/2005 |
Drug Discovery
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and presentation |
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09/12/2005 |
Workshop on Multi-Teraflop Computing in
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Website | ||
09/16/2005 |
Chemistry Review
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presentation |
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09/19/2005 |
Biomolecular Structure
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presentation |
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09/23/2005 |
Molecular Interactions and Recognition
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presentation |
rizzo.lect.005.pdf | |
MOLECULAR MODELING (5 meetings) |
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09/26/2005 |
Introduction to Thermodynamics
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presentation |
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09/30/2005 |
Stony Brook Symposium on New Horizons in Organic Chemistry
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10/03/2005 |
No Class (Rosh Hashanah) |
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10/07/2005 |
All Atom Force Fields (Molecular Mechanics)
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10/10/2005 |
Explicit Solvent Models
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10/14/2005 |
Continuum Solvent Models
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SAMPLING METHODS (5 meetings) |
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10/17/2005 |
Molecular Conformation
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10/21/2005 |
Primary Sampling Methods for Computer Simultations
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10/24/2005 |
Predicting Protein Structure I.
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10/28/2005 | Predicting Protein Structure II.
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10/31/2005 |
Enhanced Sampling Techniques
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LEAD DISCOVERY (5 meetings) |
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11/04/2005 |
Docking I.
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11/07/2005 |
Docking II.
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11/11/2005 |
Discovery Methods I.
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11/14/2005 |
Discovery Methods II.
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11/18/2005 |
Discovery Methods Applications
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LEAD REFINEMENT (5 meetings) |
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11/21/2005 |
Binding Energy I. Free Energy Perturbation (FEP)
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11/25/2005 |
No class (Thanksgiving) |
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11/28/2005 |
Binding Energy II. Linear Response
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12/02/2005 |
Binding Energy III. MM-PBSA, MM-GBSA
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12/05/2005 |
Properties of Known Drugs
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12/09/2005 |
Property Prediction
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Y. Cheng |
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12/12/2005 |
Guest Lecture
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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. |