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Biophys J. 2011 Dec 21;101(12):2966-9. doi: 10.1016/j.bpj.2011.10.054. Epub 2011 Dec 20.

Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes.

Author information

  • 1Department of Structural Biology, Stanford Medical School, Stanford, California, USA. jenelle@stanford.edu

Abstract

We present what to our knowledge is a new method of optimized torsion-angle normal-mode analysis, in which the normal modes move along curved paths in Cartesian space. We show that optimized torsion-angle normal modes reproduce protein conformational changes more accurately than Cartesian normal modes. We also show that orthogonalizing the displacement vectors from torsion-angle normal-mode analysis and projecting them as straight lines in Cartesian space does not lead to better performance than Cartesian normal modes. Clearly, protein motion is more naturally described by curved paths in Cartesian space.

PMID:
22208195
PMCID:
PMC3244061
DOI:
10.1016/j.bpj.2011.10.054
[PubMed - indexed for MEDLINE]
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