Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.

ABSTRACT: Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the "hidden" atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and ilmm) reprodu

SUBMITTER: Childers MC 

PROVIDER: S-EPMC6420231 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature