CATH: Comprehensive structural and functional annotations for genome sequences

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D376-D381

  Sillitoe, Ian ^a   Lewis, Tony E ^a   Cuff, Alison ^a   Das, Sayoni ^a   Ashford, Paul ^a   Dawson, Natalie L ^a   Furnham, Nicholas ^b   Laskowski, Roman A ^c   Lee, David ^a   Lees, Jonathan G ^a   Lehtinen, Sonja ^a   Studer, Romain A ^c   Thornton, Janet ^c   Orengo, Christine A ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CATH DATABASE; CLASSIFICATION ALGORITHM; MOLECULAR EVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN STRUCTURE; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; WEB BROWSER; CLASSIFICATION; GENETICS; GENOMICS; INTERNET; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE;

PROTEIN;

DATABASES, PROTEIN; GENOMICS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84941039390     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku947     Document Type: Article

References (19)

1. Cuff, A., Redfern, O. C., Greene, L., Sillitoe, I., Lewis, T., Dibley, M., Reid, A., Pearl, F., Dallman, T., Todd, A. et al. (2009) The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure (London, England: 1993), 17, 1051-1062.
2. Dessailly, B. H., Dawson, N. L., Mizuguchi, K. and Orengo, C. A. (2013) Functional site plasticity in domain superfamilies. Biochim. Biophys. Acta, 1834, 874-889.
3. Lee, D. A., Rentzsch, R. and Orengo, C. (2010) GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res., 38, 720-737.
4. Gene Ontology Consortium. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res., 38, D331-D335.
5. Rentzsch, R. and Orengo, C. A. (2013) Protein function prediction using domain families. BMC Bioinformat., 14(Suppl. 3), S5.
6. Schnoes, A. M., Ream, D. C., Thorman, A. W., Babbitt, P. C. and Friedberg, I. (2013) Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput. Biol., 9, e1003063.
7. Valdar, W. S. (2002) Scoring residue conservation. Proteins, 48, 227-241.
8. Capra, J. A. and Singh, M. (2008) Characterization and prediction of residues determining protein functional specificity. Bioinformatics (Oxford, England), 24, 1473-1480.
9. Bairoch, A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305.
10. Widmann, M., Radloff, R. and Pleiss, J. (2010) The Thiamine diphosphate dependent Enzyme Engineering Database: a tool for the systematic analysis of sequence and structure relations. BMC Biochem., 11, doi:10.1186/1471-2091-11-9.
11. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
12. Chandonia, J.-M. M., Hon, G., Walker, N. S., Conte, L. L., Koehl, P., Levitt, M. and Brenner, S. E. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
13. Taylor, W. R. and Orengo, C. A. (1989) Protein structure alignment. J. Mol. Biol., 208, 1-22.
14. Theobald, D. L. and Wuttke, D. S. (2006) THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics (Oxford, England), 22, 2171-2172.
15. Eddy, S. R. (2009) A new generation of homology search tools based on probabilistic inference. Genome Informat., 23, 205-211.
16. Tamuri, A. U. and Laskowski, R. A. (2010) ArchSchema: a tool for interactive graphing of related Pfam domain architectures. Bioinformatics (Oxford, England), 26, 1260-1261.
17. UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
18. Gutmanas, A., Alhroub, Y., Battle, G. M., Berrisford, J. M., Bochet, E., Conroy, M. J., Dana, J. M., Montecelo, M. A. F., Van Ginkel, G., Gore, S. P. et al. (2014) PDBe: Protein Data Bank in Europe. Nucleic Acids Res., 42, doi:10.1093/nar/gkt1180.
19. Furnham, N., Sillitoe, I., Holliday, G. L., Cuff, A. L., Rahman, S. A., Laskowski, R. A., Orengo, C. A. and Thornton, J. M. (2012) FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res., 40, D776-D782.