A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations.

ABSTRACT: Graphs are rapidly becoming a powerful and ubiquitous tool for the analysis of protein structure and for event detection in dynamical protein systems. Despite their rise in popularity, however, the graph representations employed to date have shared certain features and parameters that have not been thoroughly investigated. Here, we examine and compare variations on the construction of graph nodes and graph edges. We propose a graph representation based on chemical groups of similar atoms within a protein rather than residues or secondary structure and find that even very simple analyses using this representation form a powerful event detection system with significant advantages over residue-based graph representations. We additionally compare graph edges based on probability of contact to

SUBMITTER: Benson NC 

PROVIDER: S-EPMC3731134 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature