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Nucleic Acids Research Advance Access published online on November 29, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl959
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© 2006 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

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison Cuff*, Tim Dallman, Mark Dibley, Oliver Redfern, Frances Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton1 and Christine A. Orengo

Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK 1 European Bioinformatics Institute, Hinxton Hall Hinxton, Cambridge CB 10 IRQ, UK

*To whom correspondence should be addressed: Tel: +1 44 207 679 3890; Fax: +1 44 207 679 7193; Email: cuff{at}biochem.ucl.ac.uk

Received September 15, 2006. Revised October 23, 2006. Accepted October 24, 2006.

We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in diverse structural homologues being determined by the structural genomics initiatives, more sensitive methods have been developed for identifying boundaries in multi-domain proteins and for recognising homologues. The CATH classification update is now being driven by an integrated pipeline that links these automated procedures with validation steps, that have been made easier by the provision of information rich web pages summarising comparison scores and relevant links to external sites for each domain being classified. An analysis of the population of domains in the CATH hierarchy and several domain characteristics are presented for version 3.0. We also report an update of the CATH Dictionary of homologous structures (CATH-DHS) which now contains multiple structural alignments, consensus information and functional annotations for 1459 well populated superfamilies in CATH. CATH is directly linked to the Gene3D database which is a projection of CATH structural data onto ~2 million sequences in completed genomes and UniProt.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Present address:

Lesley H. Greene, Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard Norfolk, VA 23529-0126, USA


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