Biochemistry 444/644 - Molecular Modeling -
Fall Semester, 2005
Topics to be covered -
1. Classical vs. quantum mechanical representation of chemical bonding
and conformation.
2. Introduction to the use of Unix workstations. Text editors,
printing, shell scripts etc.
3. Internal coordinates for peptides, nucleotides, carbohydrates etc.
4. Syntax of molecular mechanics software codes (CHARMm).
Residue Topology Files, molecular mechanics parameter files.
Example of building a small peptide (enkephalin).
5. Energy minimization, normal mode analysis, adiabatic mapping
and relaxed energy maps.
6. The building of molecular models. Polymers from monomers.
Patch files.
7. Classical force field parameter development. Solvent effects
and potentials of mean force. Compact representations including extended
atoms.
8. Central repositories of macromolecular structures. Protein
Data Bank.
9. The problems of electrostatic forces in biomolecules. Cutoffs
of long range forces and effect of water as solvent.
10. The searching of conformational space. Example of random
search methods.
Monte Carlo methods and Metropolis algorithm. Umbrella sampling.
11. Molecular dynamics simulation, trajectories. The distinction
between potential energy, total energy and free energy.
12. Molecular mechanics for the interpretation of experimental data.
X-ray crystallography, NMR spectroscopy.
13. Molecular mutagenesis and free energy calculations.
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