Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture.

ABSTRACT:

Background

Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance and power testing to identify modules in protein structures. In the first step, clusters are determined by optimizing the partition that maximizes the modularity score. Second, each cluster is tested for significance. Significant clusters are referred to as modules. Evolutionary modules are identified by analyzing homologous structures. Dynamic modules are inferred from sets of snapshots of molecular simulations. We present here a methodology to identify sub-domain architecture robustly, biologically meaningful, and statistically supported.

Results

The robus

SUBMITTER: Hleap JS 

PROVIDER: S-EPMC4016585 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature