This course provides a broad and practical introduction to the major techniques employed in the computational modeling of biological structures: computational chemistry, molecular dynamics, normal mode analysis, Monte Carlo simulations, electrostatics, and conformational analysis. The course will be useful for graduate students in the pharmaceutical and medical disciplines who wish to model the physical and chemical properties of biological structures.
Topical Outline:
Session 1 Molecular Modeling Overview Reading Assignment
Session 2 Biomolecular Structure, UNIX I
Session 3 Visualization of Biomolecular Structures, UNIX II
Session 4 Molecular Dynamics Simulation: Overview, Practice I
Session 5 Molecular Dynamics Simulation: Practice II
Session 6 Molecular Dynamics Simulation: Preparation, Analysis
Session 7 Normal Mode and Principal Component Analysis
Session 8 Thermodynamics, Monte Carlo, Continuum Electrostatics
Session 9 Free Energy Calculations
Session 10 Ligand Binding, Docking, and Screening Term Project: due @ session 14
Session 11 Quantum Chemistry I
Session 12 Quantum Chemistry II
Session 13 Multi-Resolution Modeling
Session 14 Interactive Rendering, Virtual Reality
http://biomachina.org/courses/modeling/
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