An automated approach to network features of protein structure ensembles.

ABSTRACT: Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range

SUBMITTER: Bhattacharyya M 

PROVIDER: S-EPMC3795498 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature