2008 Fall Course: AMS-535Introduction to Computational Structural Biology and Drug Design |
Dr. Robert C. Rizzo |
3:50-5:10 PM, Monday and Wednesday |
Room 226, Stony Brook Union |
Course Announcement (pdf) |
Description: |
| AMS-535 provides an introduction to the field of computational structure-based drug design. No prior knowledge is assumed and all are welcome to attend. Methods and applications that use computation to model biological systems involved in human disease will be emphasized. The course aims to foster collaborative learning and will consist of presentations by the instructor, guest lecturers, and by course participants with the goal of summarizing key methods, topics, and papers relevant to the field. |
Topics: |
1. Drug Discovery and Biomolecular Structure (Chemistry Review, Proteins, Carbohydrates, Nucleic acids, Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure) |
| 2. Molecular Modeling (Thermodynamics, Classical Force Fields, Molecular Mechanics, Solvent Models, Parameter Development) |
| 3. Sampling Methods (Conformational Space, Molecular Dynamics, Monte Carlo, Sampling Techniques, Predicting Protein Structure, Protein Folding) |
| 4. Lead Discovery (Docking as a Lead Generation Tool, Algorithms, Discovery Methods, Applications) |
| 5. Lead Refinement (Free Energy Perturbation, Linear Response and Extended Linear Response, MM-PBSA and MM-GBSA , Properties of Known Drugs , Property Prediction) |
Companion Course AMS-536 (Spring Semesters): |
| 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). |
Class Schedules and Syllabus: |