CHEM 388
Molecular Modeling, Simulation and Design: Principles and Applications
CHEM 388Molecular Modeling, Simulation and Design: Principles and Applications |
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Computational methods are increasingly proving themselves to be important tools in the arsenal of research methods that can be used to understand and develop insight into the complex structure function relationships of biological systems at the molecular level. The aim of this course is to equip participants with the fundamental principles behind the modeling and simulation algorithms used for such research, covering the relevant aspects of molecular physics, structural biology and biochemistry, bioinformatics and pharmaceutical design.
The first section of the course will deal with the fundamentals of molecular modeling and simulation starting with their application to simple hard and soft sphere systems, leading to more complex models of real chemical systems based on the description of a “force field”. Different procedures involved in molecular conformational search including energy minimization, molecular dynamics and Monte Carlo simulation methods will be introduced.
In the second section, molecular dynamics simulations on protein, DNA, and RNA molecules in solution will be treated in detail, including a consideration of methods based on implicit and explicit solvent description. The various procedures available to analyze the simulation results will be covered in detail. The application of relevant computational methods in protein folding and structure prediction, DNA bending and ligand binding studies will be discussed.
The third section will cover topics of current interest in computer aided pharmaceutical research and drug design including homology modeling, QSAR models, molecular library design and topics in Cheminformatics, in silico methods used for “hit” determination and optimization of lead molecules. Free energy simulations which constitute the holy grail of molecular simulations will be covered.
A series of computer-based exercises will be providing the participants hands-on capabilities in the use of computers, molecular graphics, molecular simulation procedures and analysis.
Major Reading
MOLECULAR MODELLING: PRINCIPLES AND APPLICATIONS, Second Edition. A. R. Leach. Prentice Hall. ISBN 0-582-38210-6
COURSE FORMAT: Lecture/Discussion/Lab
Times: Tuesday, Thursday 2:40 PM - 4:00 PM Location: HA51 (John Sease Learning Center)
Course Director: Prof D. L. Beveridge
Lectures by: Dr. S. B. Dixit, Prof D. L. Beveridge
Tutor: Sergei Ponomarev
Links:
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Web page maintained by Surjit Dixit (sdixit at wesleyan dot edu) Last modified on 02/14/2006 |
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