Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.
|Title||Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.|
|Publication Type||Journal Article|
|Year of Publication||2008|
|Authors||Emperador, Agustí, Carrillo Oliver, Rueda Manuel, and Orozco Modesto|
|Date Published||2008 Sep|
|Keywords||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.