Modeling Biomolecules
Jackson State University in Jackson, MS  June 5-9, 2006
http://chemistry.gsu.edu/CWCS/bio-mod.php


Jerzy Leszczynski (Jackson State University),  

This workshop is aimed to introduce nonexpert college faculty to the 
contemporary molecular modeling techniques used in biochemistry, 
molecular biology and related fields.  The workshop is divided into 
the two 1.5 hour lectures in the mornings, and afternoon hands-on 
sessions in computer laboratory.  Lectures will be devoted to 
introduction of quantum mechanics methodology, theory of intermolecular 
interactions, molecular mechanics and dynamics with discussion of their 
applicability range and limitations and presentation of relevant case 
studies.  Laboratory sessions will cover molecular model building aided 
by the use of structural databases, optimization of biomolecular 
structures.  Particular emphasis will be directed to systematic first 
principle analysis of approximate methods used in simulation of 
interactions between biomolecules, rational de novo drug design, 
modeling chemical reactions involving biomolecules and enzyme 
catalysis.  Possible future computational projects related to 
research areas of individual participants will be discussed and 
encouraged.  The available open source software tools for molecular 
modeling will be also reviewed.

Day 1: Lecture:  Basic concepts of molecular modeling, molecular model 
building, use of structural databases (CSD, PDB, NDB)
Laboratory:  building and modifying molecular structures, structure 
analysis.

Day 2:  Lectures:  Basic concepts of quantum mechanics and overview of 
standard computational methods of quantum chemistry
Laboratory:  structure optimization, calculation of molecular properties.

Day 3: Lectures : Elements of the theory of intermolecular interactions 
used in molecular modeling, docking, rational de novo drug design;
Laboratory:  structure of molecular complexes, analysis of intermolecular 
interactions, docking.

Day 4: Lectures:  Molecular mechanics and dynamics, force fields, 
conformational analysis
Laboratory:  structure optimization of biomacromolecules, simulated 
annealing, conformational analysis, homology modeling.

Day 5:  Lectures:  Modeling of chemical reactions and enzyme catalysis. 
Overview of new emerging molecular modeling techniques, commercial and 
open source molecular modeling software.

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