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    Biophys J. 2008 Sep;95(5):2127-38. Epub 2008 May 16.

    Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.

    Source

    Molecular Modeling and Bioinformatics Unit, Joint Research Program in Computational Biology, Institute for Research in Biomedicine, Barcelona 08028, Spain.

    Abstract

    A systematic study of two coarse-grained techniques for the description of protein dynamics is presented. The two techniques exploit either Brownian or discrete molecular dynamics algorithms applied in the context of simple C(alpha)-C(alpha) potentials, like those used in coarse-grained normal mode analysis. Coarse-grained simulations of the flexibility of protein metafolds are compared to those computed with fully atomistic molecular dynamics simulations using state-of-the-art physical potentials and explicit solvent. Both coarse-grained models efficiently capture critical features of the protein dynamics.

    PMID:
    18487297
    [PubMed - indexed for MEDLINE]
    PMCID:
    PMC2517050
    Free PMC Article

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