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CABS-flex: server for fast simulation of protein structure fluctuations

2013; Oxford University Press; Volume: 41; Issue: W1 Linguagem: Inglês

10.1093/nar/gkt332

1362-4962

Michał H. Jamróz, Andrzej Koliński, Sebastian Kmiecik,

Hemoglobin structure and function

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.