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

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.

SUBMITTER: Jamroz M

PROVIDER: S-EPMC3692091 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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

Jamroz Michal M Kolinski Andrzej A Kmiecik Sebastian S

Nucleic acids research 20130508 Web Server issue

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 ...[more]

PMID: 23658222

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