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Nucleic Acids Res. 2013 Jul;41(Web Server issue):W427-31. doi: 10.1093/nar/gkt332. Epub 2013 May 8.

CABS-flex: Server for fast simulation of protein structure fluctuations.

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  • 1Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.

Abstract

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

PMID:
23658222
[PubMed - indexed for MEDLINE]
PMCID:
PMC3692091
Free PMC Article
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