Willy Wriggers
D.E. Shaw Research/Weill Cornell Medical College
"Coarse Grained Models for Molecular Structure Refinement and Dynamics"
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. Three coarse graining approaches were introduced in the last decade that are based on Delaunay tessellation-based graphs and neural network theory: (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) how to identify functionally important, rare events in long molecular dynamics (MD) trajectories. Software implementations of ideas (1-3) are freely available on the internet. Specifically, the novel Python-based package "TimeScapes", developed at D. E. Shaw Research for MD trajectory analysis, will be presented. Tests based on actual micro- to millisecond MD simulations demonstrate that the package can be used to efficiently detect and characterize important conformational changes in realistic protein systems.
References:
1. http://wriggers.biomachina.org/publications_abs/WRIG04.html
2. http://wriggers.biomachina.org/publications_abs/STEM09.html
3. http://pubs.acs.org/action/showLargeCover?issue=346432824
Software Links:
1. http://situs.biomachina.org
2. http://modehunter.biomachina.org
3. http://www.deshawresearch.com/resources_timescapes.html
Host: Chris Wiggins
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