On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

ABSTRACT: Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several forc

SUBMITTER: O'Brien ES 

PROVIDER: S-EPMC4941777 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature