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Nucleic Acids Research 2005 33(Database Issue):D183-D187; doi:10.1093/nar/gki105
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Nucleic Acids Research, 2005, Vol. 33, Database issue D183-D187
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

PDBSite: a database of the 3D structure of protein functional sites

Vladimir A. Ivanisenko*, Sergey S. Pintus, Dmitry A. Grigorovich and Nickolay A. Kolchanov

Institute of Cytology and Genetics SBRAS, Lavrentyev Avenue 10, Novosibirsk 630090, Russia

* To whom correspondence should be addressed. Tel: +7 3832332971; Fax: +7 3832331278; Email: salix{at}bionet.nsc.ru

Received August 18, 2004; Revised and Accepted October 15, 2004

The PDBSite database provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein–protein, protein–DNA and protein–RNA interactions) in the Protein Data Bank (PDB). The PDBSite is available online at http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/. It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure. The PDBSite is updated after each new PDB release.

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