CABS-fold: Server for the de novo and consensus-based prediction of protein structure.

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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.

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Blaszczyk, M., Jamroz, M., Kmiecik, S., & Kolinski, A. (2013). CABS-fold: Server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Research, 41(Web Server issue). https://doi.org/10.1093/nar/gkt462

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