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Nucleic Acids Research Advance Access published online on November 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm1019
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© 2007
The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Gene3D: comprehensive structural and functional annotation of genomes

Corin Yeats1,*, Jonathan Lees1, Adam Reid1, Paul Kellam1, Nigel Martin2, Xinhui Liu1 and Christine Orengo1

1UCL, Department of Molecular Biology & Biochemistry, Darwin Building, Gower St, London WC1E 6BT and 2School of Computer Science and Information Systems, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK

*To whom correspondence should be addressed. Tel: +02076793890; Fax: +02076797193; Email: yeats{at}biochem.ucl.ac.uk

Received September 14, 2007. Revised October 23, 2007. Accepted October 27, 2007.

Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein–protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/


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