An information theory-based tool for characterizing the interaction environment of a protein

Abstract

In recent years large amounts of information have been accumulated in proteomic, genetic and metabolic databases. Much effort has been dedicated to developing methods that successfully exploit, organize and structure this information. However, there is no application, that we know of, that semantically characterizes the interaction environment in which a protein exists. A high-throughput software package has been developed to retrieve information from publicly available databases, such as the Gene Ontology Annotation (GOA) database and the Human Proteome Resource Database (HPRD) and structure their information. This information is presented to the user as groups of semantically described dense interaction subnetworks that interact with a target protein.