NAR Molecular Biology Database Collection entry number 943

http://www.ces.clemson.edu/compbio/protcom

Petras J. Kundrotas and Emil Alexov

Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, SC29634 USA

Contact pkundro@clemson.edu

The database of protein complexes (PROTCOM) contains known 3D structures of two-chain protein complexes enriched with two-domain structures artificially created from 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 original PDB files for the domain structures are modified in order to mimic two-chain protein complexes. The database could be used for benchmarking purposes of the docking and other algorithms of 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. The database provides an integrated set of tools for browsing, searching (combination of up to ten different criteria), visualizing and downloading a pool of database entries.

As of July 2006 the database contains 1770 entries (967 protein-protein complexes and 804 domain-domain structures), 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. The work is currently in progress in order to include multi-chain protein complexesand multi-domain structures.

1. Kundrotas P.J. and Alexov E. (2006) Predictimg 3D structures of transient protein-protein complexes by homology, Biochimica et Biophysica Acta, 1764: 1498 - 1511.
2. Kundrotas P.J. and Alexov E. (2007) PROTCOM: Searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Research 35 (Database issue): in press

Go to the abstract in the NAR 2007 Database Issue.

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