PROTCOM: Searchable database of protein complexes enhanced with domain-domain structures

Abstract

The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein-protein complexes enriched with artificially created domain-domain structures using the available entries in the Protein Data Bank. The domain-domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/ compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein-protein complexes. The database can be utilized as a template database in the homology or threading methods for modeling the 3D structures of unknown protein-protein complexes. PROTCOM provides the scientific community with an integrated set of tools for browsing, searching, visualizing and downloading a pool of protein complexes. The user is given the option to select a subset of entries using a combination of up to 10 different criteria. As on July 2006 the database contains 1770 entries, each of which consists of the known 3D structures and additional relevant information that can be displayed either in text-only or in visual mode. © 2007 Oxford University Press.