A natural coarse graining for simulating large biomolecular motion

Holger Gohlke, Michael Thorpe

Research output: Contribution to journalArticlepeer-review

114 Scopus citations

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 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.

Original languageEnglish (US)
Pages (from-to)2115-2120
Number of pages6
JournalBiophysical journal
Volume91
Issue number6
DOIs
StatePublished - 2006

ASJC Scopus subject areas

  • Biophysics

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