MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories.

ABSTRACT:

Background

Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface.

Results

On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between diffe

SUBMITTER: Abdel-Azeim S 

PROVIDER: S-EPMC4095001 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature