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Nucleic Acids Research 2005 33(Database Issue):D247-D251; doi:10.1093/nar/gki024
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Nucleic Acids Research, 2005, Vol. 33, Database issue D247-D251
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Frances Pearl, Annabel Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony Lewis, Christopher Bennett, Russell Marsden, Alistair Grant, David Lee*, Adrian Akpor, Michael Maibaum, Andrew Harrison, Timothy Dallman, Gabrielle Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet Thornton1 and Christine Orengo

Biochemistry and Molecular Biology Department, University College London, University of London, Gower Street, London WC1E 6BT, UK and 1 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

* To whom correspondence should be addressed. Tel: +44 20 7679 3890; Fax: +44 20 7679 7193; Email: dlee{at}biochem.ucl.ac.uk
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received September 15, 2004; Revised and Accepted September 21, 2004

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43 229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616 470 domain sequences classified into 23 876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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