Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.

ABSTRACT: Molecular dynamics (MD) simulation is a well-established tool for the computational study of protein structure and dynamics, but its application to the important problem of protein structure prediction remains challenging, in part because extremely long timescales can be required to reach the native structure. Here, we examine the extent to which the use of low-resolution information in the form of residue-residue contacts, which can often be inferred from bioinformatics or experimental studies, can accelerate the determination of protein structure in simulation. We incorporated sets of 62, 31, or 15 contact-based restraints in MD simulations of ubiquitin, a benchmark system known to fold to the native state on the millisecond timescale in unrestrained simulations. One-third of the restrai

SUBMITTER: Raval A 

PROVIDER: S-EPMC4815320 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature