Nucleic Acids Research, 2000, Vol. 28, No. 1 277-282
© 2000 Oxford University Press
Assigning genomic sequences to CATH
1Department of Biochemistry and Molecular Biology, University College London, University of London, Gower Street, London WC1E 6BT, UK and 2Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
We report the latest release (version 1.6) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath ). This is a hierarchical classification of 18 577 domains into evolutionary families and structural groupings. We have identified 1028 homologous superfamilies in which the proteins have both structural, and sequence or functional similarity. These can be further clustered into 672 fold groups and 35 distinct architectures. Recent developments of the database include the generation of 3D templates for recognising structural relatives in each fold group, which has led to significant improvements in the speed and accuracy of updating the database and also means that less manual validation is required. We also report the establishment of the CATH-PFDB (Protein Family Database), which associates 1D sequences with the 3D homologous superfamilies. Sequences showing identifiable homology to entries in CATH have been extracted from GenBank using PSI-BLAST. A CATH-PSIBLAST server has been established, which allows you to scan a new sequence against the database. The CATH Dictionary of Homologous Superfamilies (DHS), which contains validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies, has been updated to include annotations associated with sequence relatives identified in GenBank. The DHS is a powerful tool for considering the variation of functional properties within a given CATH superfamily and in deciding what functional properties may be reliably inherited by a newly identified relative.
* To whom correspondence should be addressed. Tel: +44 20 7419 3890; Fax: +44 20 7380 7193; Email: frances@biochem.ucl.ac.uk
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. R. Jefferson, T. P. Walsh, T. J. Roberts, and G. J. Barton SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions Nucleic Acids Res., January 12, 2007; 35(suppl_1): D580 - D589. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. W. Janes Bioinformatics analyses of circular dichroism protein reference databases Bioinformatics, December 1, 2005; 21(23): 4230 - 4238. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Cheng, A. Z. Randall, M. J. Sweredoski, and P. Baldi SCRATCH: a protein structure and structural feature prediction server Nucleic Acids Res., July 1, 2005; 33(suppl_2): W72 - W76. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez InterProScan: protein domains identifier Nucleic Acids Res., July 1, 2005; 33(suppl_2): W116 - W120. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Ausiello, A. Zanzoni, D. Peluso, A. Via, and M. Helmer-Citterich pdbFun: mass selection and fast comparison of annotated PDB residues Nucleic Acids Res., July 1, 2005; 33(suppl_2): W133 - W137. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Sillitoe, M. Dibley, J. Bray, S. Addou, and C. Orengo Assessing strategies for improved superfamily recognition Protein Sci., July 1, 2005; 14(7): 1800 - 1810. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Liu, Z. Li, Y. Chiang, T. Acton, G. T. Montelione, D. Murray, and T. Szyperski High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases Protein Sci., June 1, 2005; 14(6): 1597 - 1608. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Tocilj, J. D. Schrag, Y. Li, B. L. Schneider, L. Reitzer, A. Matte, and M. Cygler Crystal Structure of N-Succinylarginine Dihydrolase AstB, Bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli J. Biol. Chem., April 22, 2005; 280(16): 15800 - 15808. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Yuan and C. Bystroff Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins Bioinformatics, April 1, 2005; 21(7): 1010 - 1019. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-M. Shin and D.-H. Cho PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures Nucleic Acids Res., January 1, 2005; 33(suppl_1): D238 - D241. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, D. Barrell, R. Apweiler, and K. Henrick E-MSD: an integrated data resource for bioinformatics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D262 - D265. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Laskowski, V. V. Chistyakov, and J. M. Thornton PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids Nucleic Acids Res., January 1, 2005; 33(suppl_1): D266 - D268. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-S. Han, H.-S. Kim, W.-H. Jang, S.-D. Lee, and J.-K. Suh PreSPI: a domain combination based prediction system for protein-protein interaction Nucleic Acids Res., December 1, 2004; 32(21): 6312 - 6320. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. V. Lunin, C. Munger, J. Wagner, Z. Ye, M. Cygler, and M. Sacher The Structure of the MAPK Scaffold, MP1, Bound to Its Partner, p14: A COMPLEX WITH A CRITICAL ROLE IN ENDOSOMAL MAP KINASE SIGNALING J. Biol. Chem., May 28, 2004; 279(22): 23422 - 23430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N.-V. Buchete, J. E. Straub, and D. Thirumalai Orientational potentials extracted from protein structures improve native fold recognition Protein Sci., April 1, 2004; 13(4): 862 - 874. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Tavoulari, S. Frillingos, P. Karatza, I. E. Messinis, and K. Seferiadis The recombinant subdomain IIIB of human serum albumin displays activity of gonadotrophin surge-attenuating factor Hum. Reprod., April 1, 2004; 19(4): 849 - 858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Lee, S. Fefeu, A. A. Edo-Ukeh, C. A. Orengo, and C. Slingsby EyeSite: a semi-automated database of protein families in the eye Nucleic Acids Res., January 1, 2004; 32(90001): D148 - 152. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Matsuura, A. Ernst, and A. Pluckthun Construction and characterization of protein libraries composed of secondary structure modules Protein Sci., November 1, 2002; 11(11): 2631 - 2643. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Yee, X. Chang, A. Pineda-Lucena, B. Wu, A. Semesi, B. Le, T. Ramelot, G. M. Lee, S. Bhattacharyya, P. Gutierrez, et al. An NMR approach to structural proteomics PNAS, February 19, 2002; 99(4): 1825 - 1830. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. M.G. Pearl, D. Lee, J. E. Bray, D. W.A. Buchan, A. J. Shepherd, and C. A. Orengo The CATH extended protein-family database: Providing structural annotations for genome sequences Protein Sci., February 1, 2002; 11(2): 233 - 244. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Mallika, A. Bhaduri, and R. Sowdhamini PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies Nucleic Acids Res., January 1, 2002; 30(1): 284 - 288. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Nagano, C. T. Porter, and J. M. Thornton The ({beta}{alpha})8 glycosidases: sequence and structure analyses suggest distant evolutionary relationships Protein Eng. Des. Sel., November 1, 2001; 14(11): 845 - 855. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. V. Grishin KH domain: one motif, two folds Nucleic Acids Res., February 1, 2001; 29(3): 638 - 643. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Alba, D. Lee, F. M. G. Pearl, A. J. Shepherd, N. Martin, C. A. Orengo, and P. Kellam VIDA: a virus database system for the organization of animal virus genome open reading frames Nucleic Acids Res., January 1, 2001; 29(1): 133 - 136. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Laskowski PDBsum: summaries and analyses of PDB structures Nucleic Acids Res., January 1, 2001; 29(1): 221 - 222. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.E. Bray, A.E. Todd, F.M.G. Pearl, J.M. Thornton, and C.A. Orengo The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues Protein Eng. Des. Sel., March 1, 2000; 13(3): 153 - 165. [Abstract] [Full Text] [PDF]
|
|