The CATH Domain Structure Database: New Protocols and Classification Levels Give a More Comprehensive Resource for Exploring Evolution

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Dec 1

PMID 17135200

Citations 140

Authors

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 Thornton

Christine A Orengo

Affiliations

Soon will be listed here.

Abstract

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 approximately 2 million sequences in completed genomes and UniProt.

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