Forum 01/07/2010

“Coarse-Grained Computer Models for Integrative Molecular Structure Refinement and Dynamics”

Willy Wriggers, Ph.D. – D. E. Shaw Research and Dept. of Biophysics and Physiology, Weill Cornell Medical College New York

An important problem in the structure determination, analysis, and simulation of complex biological systems will be described: how to reduce the complexity of biomolecules to spatial scales that are well suited for particular modeling applications. In this short overview, focused on topics in integrative biology and imaging, I will briefly discuss three coarse-graining approaches which were introduced in the last decade: (1) the fitting of molecular fragments into large macromolecular complexes from low-resolution electron microscopy, (2) an elastic rod model for normal mode analysis of any three-dimensional graph irrespective of the atom connectedness, and (3) a technique to identify functionally important, rare events in long molecular dynamics (MD) trajectories.