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Biophys. J. BioFAST: First Published June 30, 2006. doi:10.1529/biophysj.106.083568
© 2006 by the Biophysical Society.

A more recent version of this article appeared on September 15, 2006.
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BIOPHYSICAL THEORY AND MODELING

A Natural Coarse Graining for Simulating Large Biomolecular Motion

Holger Gohlke 1 and Michael Thorpe 2*

1 J. W. Goethe-University
2 Arizona State University

* To whom correspondence should be addressed. E-mail: michael.thorpe{at}asu.edu.

Submitted on February 16, 2006
Revised on March 29, 2006
Accepted on 14 June 2006


  Abstract
Various coarse graining schemes have been proposed to speed up computer simulations of the motion within large biomolecules, which can contain hundreds of thousands of atoms. We point out here that there is very natural way of doing this, using the rigid regions identified within a biomolecule as the coarse grain elements. Subsequently, computer resources can be concentrated on the flexible connections between the rigid units. Examples of the use of such techniques are given for the protein barnase, using the geometric simulation technique FRODA and the rigidity enhanced elastic network model RCNMA to compute mobilities.

Key Words: coarse graining, dynamics, flexibility, proteins, rigid regions




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Copyright © 2006 by the Biophysical Society.