ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.

Abstract

Most proteins lack experimentally validated functions. To address this problem, we implemented the Evolutionary Trace Annotation (ETA) method in the Cytoscape network visualization environment. The result is the ETAscape plugin, which builds a structural genomics network based on local structural and evolutionary similarities among proteins and then globally diffuses known annotations across the resulting network. The plugin displays these novel functional annotations, their confidence, the molecular basis for individual matches and the set of matches that lead to a prediction. The ETA Network Plugin is available publicly for download at http://mammoth.bcm.tmc.edu/networks/.