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Originally published as Biophys J. BioFAST on June 30, 2006.
doi:10.1529/biophysj.106.083568
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Biophysical Journal 91:2115-2120 (2006)
© 2006 The Biophysical Society

A Natural Coarse Graining for Simulating Large Biomolecular Motion

Holger Gohlke * and M. F. Thorpe {dagger}

* Department of Biological Sciences, J. W. Goethe-University, Frankfurt, Germany; and {dagger} Center for Biological Physics, Bateman Physical Sciences, Arizona State University, Tempe, Arizona

Correspondence: Address reprint requests to M. F. Thorpe, Center for Biological Physics, Bateman Physical Sciences, Arizona State University, Tempe, AZ 85287-1504. Tel.: 480-965-3085; Fax: 480-965-4669; E-mail: mft{at}asu.edu.

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 a 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 and the maltodextrin binding protein, using the geometric simulation technique FRODA and the rigidity enhanced elastic network model RCNMA to compute mobilities and atomic displacements.




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