Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.
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.
Emperador
Agustí
A
Molecular Modeling and Bioinformatics Unit, Joint Research Program in Computational Biology, Institute for Research in Biomedicine, Barcelona 08028, Spain.
Carrillo
Oliver
O
Rueda
Manuel
M
Orozco
Modesto
M
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D011487:Protein Conformation