Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent.

ABSTRACT: The millisecond time scale needed for molecular dynamics simulations to approach the quantitative study of protein folding is not yet routine. One approach to extend the simulation time scale is to perform long simulations on specialized and expensive supercomputers such as Anton. Ideally, however, folding simulations would be more economical while retaining reasonable accuracy, and provide feedback on structure, stability and function rapidly enough if partnered directly with experiment. Approaches to this problem typically involve varied compromises between accuracy, precision, and cost; the goal here is to address whether simple implicit solvent models have become sufficiently accurate for their weaknesses to be offset by their ability to rapidly provide much more precise conformational

SUBMITTER: Nguyen H 

PROVIDER: S-EPMC4195377 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature