Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories.

ABSTRACT: Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD) trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF) about the average position of residues defined by Cα-atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. Thes

SUBMITTER: Farmer J 

PROVIDER: S-EPMC6258182 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature