Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization.

ABSTRACT: Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-

SUBMITTER: Shirvanyants D 

PROVIDER: S-EPMC3406226 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature