Folding of small proteins using constrained molecular dynamics.

ABSTRACT: The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward "native-like" structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement. It is computationally expensive to perform all-atom simulations of protein folding because the processes occur on a time scale of microseconds. Compared to the all-atom MD simulation, constrained MD methods have the advantage that stable dynamics can be achieved for larger time steps and the number of degrees of freedom is an order of magnitude smaller, leading to a decrease in computational cost. We have developed a generalized constrain

SUBMITTER: Balaraman GS 

PROVIDER: S-EPMC3124276 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature