Journal
BIOPHYSICAL JOURNAL
Volume 91, Issue 6, Pages 2115-2120Publisher
CELL PRESS
DOI: 10.1529/biophysj.106.083568
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Funding
- NIGMS NIH HHS [R01 GM067249, GM 067249] Funding Source: Medline
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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. exible 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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