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: Lecture: Basic concepts of quantum mechanics and overview of standard computational methods of quantum chemistry. Laboratory: structure optimization, calculation of molecular properties.
Day 3: Lecture: 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: Lecture: Molecular mechanics and dynamics, force fields, conformational analysis. Laboratory: structure optimization of biomacromolecules, simulated annealing, conformational analysis, homology modeling.
Day 5: Lecture: Modeling of chemical reactions and enzyme catalysis. Overview of new emerging molecular modeling techniques, commercial and open source molecular modeling software.