Developing a molecular dynamics force field for both folded and disordered protein states.

ABSTRACT: Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensiti

SUBMITTER: Robustelli P 

PROVIDER: S-EPMC6003505 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature