Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.
|Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.
|Year of Publication
|Emperador, Agustí, Carrillo Oliver, Rueda Manuel, and Orozco Modesto
|Algorithms, Computer Simulation, Models, Molecular, Protein Conformation
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.