Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.

ABSTRACT: Given the large number of crystal structures and NMR ensembles that have been solved to date, classical molecular dynamics (MD) simulations have become powerful tools in the atomistic study of the kinetics and thermodynamics of biomolecular systems on ever increasing time scales. By virtue of the high-dimensional conformational state space that is explored, the interpretation of large-scale simulations faces difficulties not unlike those in the big data community. We address this challenge by introducing a method called clustering based feature selection (CB-FS) that employs a posterior analysis approach. It combines supervised machine learning (SML) and feature selection with Markov state models to automatically identify the relevant degrees of freedom that separate conformational states.

SUBMITTER: Sultan MM 

PROVIDER: S-EPMC4263461 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature