An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.

ABSTRACT: Proteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to use the centers of mass of the side chains as nodes. It becomes thus critical to evaluate the minimal distance cutoff between the centers of mass which will provide stable network properties. Moreover, when the PSN is derived from a structural ensemble collected by molecular dynamics (MD), the impact

SUBMITTER: Salamanca Viloria J 

PROVIDER: S-EPMC5460117 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature