Forging tools for refining predicted protein structures.

ABSTRACT: Refining predicted protein structures with all-atom molecular dynamics simulations is one route to producing, entirely by computational means, structural models of proteins that rival in quality those that are determined by X-ray diffraction experiments. Slow rearrangements within the compact folded state, however, make routine refinement of predicted structures by unrestrained simulations infeasible. In this work, we draw inspiration from the fields of metallurgy and blacksmithing, where practitioners have worked out practical means of controlling equilibration by mechanically deforming their samples. We describe a two-step refinement procedure that involves identifying collective variables for mechanical deformations using a coarse-grained model and then sampling along these deformation

SUBMITTER: Lin X 

PROVIDER: S-EPMC6511001 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature