The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
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.
Pearl
Frances
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Biochemistry and Molecular Biology Department, University College London, University of London, Gower Street, London WC1E 6BT, UK.
Todd
Annabel
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Sillitoe
Ian
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Dibley
Mark
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Redfern
Oliver
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Lewis
Tony
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Bennett
Christopher
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Marsden
Russell
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Grant
Alistair
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Lee
David
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Akpor
Adrian
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Maibaum
Michael
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Harrison
Andrew
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Dallman
Timothy
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Reeves
Gabrielle
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Diboun
Ilhem
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Addou
Sarah
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Lise
Stefano
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Johnston
Caroline
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Sillero
Antonio
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Thornton
Janet
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Orengo
Christine
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D030561:Databases, Nucleic Acid; D030562:Databases, Protein / Q000706:statistics & numerical data; D023281:Genomics; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000145:classification* / Q000235:genetics; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D018511:Systems Integration; D014584:User-Computer Interface
D011506:Proteins