Nucleic Acids Research Advance Access originally published online on November 29, 2006
Nucleic Acids Research 2007 35(Database issue):D291-D297; doi:10.1093/nar/gkl959
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, Database issue D291-D297
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK 1 European Bioinformatics Institute, Hinxton Hall Hinxton, Cambridge CB 10 IRQ, UK
*To whom correspondence should be addressed: Tel: +1 44 207 679 3890; Fax: +1 44 207 679 7193; Email: cuff{at}biochem.ucl.ac.uk
Received September 15, 2006. Revised October 23, 2006. Accepted October 24, 2006.
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 
2 million sequences in completed genomes and UniProt.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Lesley H. Greene, Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard Norfolk, VA 23529-0126, USA
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, et al. PDBe: Protein Data Bank in Europe Nucleic Acids Res., October 25, 2009; (2009) gkp916v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Skolnick, A. K. Arakaki, S. Y. Lee, and M. Brylinski The continuity of protein structure space is an intrinsic property of proteins PNAS, September 15, 2009; 106(37): 15690 - 15695. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Skolnick and M. Brylinski FINDSITE: a combined evolution/structure-based approach to protein function prediction Brief Bioinform, July 1, 2009; 10(4): 378 - 391. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. W. Brandt and J. Heringa webPRC: the Profile Comparer for alignment-based searching of public domain databases Nucleic Acids Res., July 1, 2009; 37(suppl_2): W48 - W52. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Fornes, R. Aragues, J. Espadaler, M. A. Marti-Renom, A. Sali, and B. Oliva ModLink+: improving fold recognition by using protein-protein interactions Bioinformatics, June 15, 2009; 25(12): 1506 - 1512. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Minasov, S. Padavattan, L. Shuvalova, J. S. Brunzelle, D. J. Miller, A. Basle, C. Massa, F. R. Collart, T. Schirmer, and W. F. Anderson Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains J. Biol. Chem., May 8, 2009; 284(19): 13174 - 13184. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. A Reeves, D. Talavera, and J. M Thornton Genome and proteome annotation: organization, interpretation and integration J R Soc Interface, February 6, 2009; 6(31): 129 - 147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Gunther, J. von Eichborn, P. May, and R. Preissner JAIL: a structure-based interface library for macromolecules Nucleic Acids Res., January 1, 2009; 37(suppl_1): D338 - D341. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Bauer, S. Gunther, D. Jansen, C. Heeger, P. F. Thaben, and R. Preissner SuperSite: dictionary of metabolite and drug binding sites in proteins Nucleic Acids Res., January 1, 2009; 37(suppl_1): D195 - D200. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Laskowski PDBsum new things Nucleic Acids Res., January 1, 2009; 37(suppl_1): D355 - D359. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Cuff, I. Sillitoe, T. Lewis, O. C. Redfern, R. Garratt, J. Thornton, and C. A. Orengo The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies Nucleic Acids Res., January 1, 2009; 37(suppl_1): D310 - D314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Csaba, F. Birzele, and R. Zimmer Protein structure alignment considering phenotypic plasticity Bioinformatics, August 15, 2008; 24(16): i98 - i104. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Ferrada and A. Wagner Protein robustness promotes evolutionary innovations on large evolutionary time-scales Proc R Soc B, July 22, 2008; 275(1643): 1595 - 1602. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. W. Brandt, J. Heringa, and J. A. M. Leunissen SEQATOMS: a web tool for identifying missing regions in PDB in sequence context Nucleic Acids Res., July 1, 2008; 36(suppl_2): W255 - W259. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Sippl, S. J. Suhrer, M. Gruber, and M. Wiederstein A discrete view on fold space Bioinformatics, March 15, 2008; 24(6): 870 - 871. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Sippl and M. Wiederstein A note on difficult structure alignment problems Bioinformatics, February 1, 2008; 24(3): 426 - 427. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. H. Dessailly, M. F. Lensink, C. A. Orengo, and S. J. Wodak LigASite a database of biologically relevant binding sites in proteins with known apo-structures Nucleic Acids Res., January 11, 2008; 36(suppl_1): D667 - D673. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Heger, E. Korpelainen, T. Hupponen, K. Mattila, V. Ollikainen, and L. Holm PairsDB atlas of protein sequence space Nucleic Acids Res., January 11, 2008; 36(suppl_1): D276 - D280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Yeats, J. Lees, A. Reid, P. Kellam, N. Martin, X. Liu, and C. Orengo Gene3D: comprehensive structural and functional annotation of genomes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D414 - D418. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Huhne, F.-T. Koch, and J. Suhnel A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules Brief Funct Genomic Proteomic, October 23, 2007; (2007) elm020v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Reid, C. Yeats, and C. A. Orengo Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone Bioinformatics, September 15, 2007; 23(18): 2353 - 2360. [Abstract] [Full Text] [PDF]
|
|