DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.

ABSTRACT: The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational pr

SUBMITTER: Lakkaraju SK 

PROVIDER: S-EPMC4756637 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature