A rapid classification protocol for the CATH Domain Database to support structural genomics

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.

[1]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[2]  M. Gerstein,et al.  Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. , 2000, Journal of molecular biology.

[3]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[4]  M. L. Jones,et al.  PDBsum: a Web-based database of summaries and analyses of all PDB structures. , 1997, Trends in biochemical sciences.

[5]  D. Haussler,et al.  Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.

[6]  J M Thornton,et al.  Domain assignment for protein structures using a consensus approach: Characterization and analysis , 1998, Protein science : a publication of the Protein Society.

[7]  C. Orengo.  CORA—Topological fingerprints for protein structural families , 2008, Protein science : a publication of the Protein Society.

[8]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[9]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[10]  Alejandro A. Schäffer,et al.  IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices , 1999, Bioinform..

[11]  W R Taylor,et al.  Fast structure alignment for protein databank searching , 1992, Proteins.