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The CATH database.

ABSTRACT: The CATH database provides hierarchical classification of protein domains based on their folding patterns. Domains are obtained from protein structures deposited in the Protein Data Bank and both domain identification and subsequent classification use manual as well as automated procedures. The accompanying website (www.cathdb.info) provides an easy-to-use entry to the classification, allowing for both browsing and downloading of data. Here, we give a brief review of the database, its corresponding website and some related tools.

SUBMITTER: Knudsen M

PROVIDER: S-EPMC3525972 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature

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The CATH database.

Knudsen Michael M Wiuf Carsten C

Human genomics 20100201 3

The CATH database provides hierarchical classification of protein domains based on their folding patterns. Domains are obtained from protein structures deposited in the Protein Data Bank and both domain identification and subsequent classification use manual as well as automated procedures. The accompanying website (www.cathdb.info) provides an easy-to-use entry to the classification, allowing for both browsing and downloading of data. Here, we give a brief review of the database, its correspond ...[more]

PMID: 20368142

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Project description:In order to support the structural genomic initiatives, both by rapidly classifying newly determined structures and by suggesting suitable targets for structure determination, we have recently developed several new protocols for classifying structures in the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath). These aim to increase the speed of classification of new structures using fast algorithms for structure comparison (GRATH) and to improve the sensitivity in recognising distant structural relatives by incorporating sequence information from relatives in the genomes (DomainFinder). In order to ensure the integrity of the database given the expected increase in data, the CATH Protein Family Database (CATH-PFDB), which currently includes 25,320 structural domains and a further 160,000 sequence relatives has now been installed in a relational ORACLE database. This was essential for developing more rigorous validation procedures and for allowing efficient querying of the database, particularly for genome analysis. The associated Dictionary of Homologous Superfamilies [Bray,J.E., Todd,A.E., Pearl,F.M.G., Thornton,J.M. and Orengo,C.A. (2000) Protein Eng., 13, 153-165], which provides multiple structural alignments and functional information to assist in assigning new relatives, has also been expanded recently and now includes information for 903 homologous superfamilies. In order to improve coverage of known structures, preliminary classification levels are now provided for new structures at interim stages in the classification protocol. Since a large proportion of new structures can be rapidly classified using profile-based sequence analysis [e.g. PSI-BLAST: Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures.

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The CATH database.

Publications

The CATH database.

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