The CATH database: an extended protein family resource for structural and functional genomics | Zendy

Frances M. G. Pearl | Zendy; C. F. Bennett | Zendy; James E. Bray | Zendy; Andrew Harrison | Zendy; Nigel Martin | Zendy; Adrian J. Shepherd | Zendy; Ian Sillitoe | Zendy; Janet M. Thornton | Zendy; Christine Orengo | Zendy

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The CATH database: an extended protein family resource for structural and functional genomics

Author(s) -

Frances M. G. Pearl,

C. F. Bennett,

James E. Bray,

Andrew Harrison,

Nigel Martin,

Adrian J. Shepherd,

Ian Sillitoe,

Janet M. Thornton,

Christine Orengo

Publication year - 2003

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkg062

Subject(s) - domain (mathematical analysis) , biology , sequence (biology) , bottleneck , genbank , database , genomics , structural genomics , sequence alignment , computational biology , computer science , genetics , genome , protein structure , peptide sequence , gene , mathematics , mathematical analysis , biochemistry , embedded system

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families. Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient sequence search protocols and reliable thresholds. This extended resource, known as the CATH-protein family database (CATH-PFDB) contains a total of 310 000 domain sequences classified into 26 812 sequence families. New sequence search protocols have been designed, based on these intermediate sequence libraries, to allow more regular updating of the classification. Further developments include the adaptation of a recently developed method for rapid structure comparison, based on secondary structure matching, for domain boundary assignment. The philosophy behind CATHEDRAL is the recognition of recurrent folds already classified in CATH. Benchmarking of CATHEDRAL, using manually validated domain assignments, demonstrated that 43% of domains boundaries could be completely automatically assigned. This is an improvement on a previous consensus approach for which only 10-20% of domains could be reliably processed in a completely automated fashion. Since domain boundary assignment is a significant bottleneck in the classification of new structures, CATHEDRAL will also help to increase the frequency of CATH updates.

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