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General Information

These Web pages are designed primarily for a course entitled "Molecular Modeling of Proteins and Nucleic Acids" taught in the Department of Biochemistry at Virginia Tech by Dr. David R. Bevan. The purpose of the course is to prepare students to read and interpret the molecular modeling literature and to apply molecular modeling in their research. The Web pages serve as a guide to students in the course, though they also may be of interest to other molecular modelers.

For several of the topics, on-line references are already available and can be accessed from links that are provided. Most notably, the excellent on-line resource developed at the NIH is referenced several times. For some topics, on-line material is not available or is unsuitable for this course. In these cases, a more comprehensive review has been prepared.

Topics

UNIX	Protein Structure and Proteomics	Nucleic Acids
Visualization	Molecular mechanics	Quantum mechanics
Geometry optimization	Molecular dynamics	Conformational searching
Homology modeling	Statistical mechanics	Free energy simulations
Docking	QSAR & Drug design	Student Presentations

General References for Molecular Modeling

Listed below are some general references that pertain to molecular modeling. References to on-line and printed resources that pertain to the specific topics are given with the topics.

On-Line References

Center for Molecular Modeling at NIH
An Introduction to Molecular Modeling by Allen Richon
Expert Protein Analysis System (ExPASy) Molecular Biology Server
MIA ??? Molecular Information Agent ??? Links to biological databases with information about macromolecules
CMS Molecular Biology Resource

Printed References

Grant, G.H. and Richards, W.G. (1995) Computational Chemistry, Oxford University Press, Oxford, 90pp.

Leach, A.R. (2001) Molecular Modelling - Principles and Applications, 2^nd edition. Prentice Hall, 744pp.

McCammon, J.A. and Harvey, S.C. (1987) Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, 234pp.

Young, D.C. (2001) Computational Chemistry ??? A Practical Guide for Applying Techniques to Real-World Problemsm, Wiley-Interscience, 381pp.