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

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.

SUBMITTER: Emperador A

PROVIDER: S-EPMC2517050 | biostudies-other | 2008 Sep

REPOSITORIES: biostudies-other

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

Emperador Agustí A Carrillo Oliver O Rueda Manuel M Orozco Modesto M

Biophysical journal 20080516 5

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 potentia ...[more]

PMID: 18487297

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