The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Furnham, Nicholas ^a   Holliday, Gemma L ^a,c   De Beer, Tjaart A P ^a   Jacobsen, Julius O B ^a,d   Pearson, William R ^b   Thornton, Janet M ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF VIRGINIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CATALYSIS; CATALYTIC SITE ATLAS 2.0 DATABASE; COMPUTER INTERFACE; DATA ANALYSIS; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME MECHANISM ONTOLOGY DATABASE; ENZYME STRUCTURE; INFORMATION PROCESSING; KNOWLEDGE BASE; MECHANISM ANNOTATION AND CLASSIFICATION IN ENZYMES DATABASE; ONTOLOGY; PRIORITY JOURNAL; PROTEIN DATABASE; RESIDUE ANALYSIS; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; UNIPROT KNOWLEDGE BASE; CATALOGING DATABASE; ENZYME ANALYSIS; BIOLOGICAL ONTOLOGY; CHEMISTRY; INTERNET;

ENZYME;

BIOLOGICAL ONTOLOGIES; CATALYTIC DOMAIN; DATABASES, PROTEIN; ENZYMES; INTERNET; SEQUENCE ANALYSIS, PROTEIN;

EID: 84891800735     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1243     Document Type: Article

References (14)

1. Uniprot Consortium. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
2. Porter, C.T., Bartlett, G.J. and Thornton, J.M. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res., 32, D129-D133.
3. Velankar, S., Alhroub, Y., Best, C, Caboche, S., Conroy, M.J., Dana, J.M., Fernandez Montecelo, M.A., van Ginkel, G., Golovin, A., Gore, S.P. et al. (2012) PDBe: Protein Data Bank in Europe. Nucleic Acids Res., 40, D445-D452.
4. Holliday, G.L., Andreini, C, Fischer, J.D., Rahman, S.A., Almonacid, D.E., Williams, S.T. and Pearson, W.R. (2012) MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res., 40, D783-D789.
5. Rahman, S., Bashton, M., Holliday, G., Schrader, R. and Thornton, J. (2009) Small Molecule Subgraph Detector (SMSD) toolkit. J. Cheminform., 1, 12.
6. Laskowski, R.A. (2009) PDBsum new things. Nucleic Acids Res., 37, D355-D359.
7. Fleischmann, A., Darsow, M., Degtyarenko, K., Fleischmann, W., Boyce, S., Axelsen, K.B., Bairoch, A., Schomburg, D., Tipton, K.F. and Apweiler, R. (2004) IntEnz, the integrated relational enzyme database. Nucleic Acids Res., 32, D434-D437.
8. International Union of Biochemistry and Molecular Biology, Nomenclature, C. and Webb, E.C. (1992) Enzyme Nomenclature 1992 : recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes/Prepared for NC-IUBMB by Edwin C. Webb. Published for the International Union of Biochemistry and Molecular Biology by Academic Press, San Diego.
9. Gomez, J., Garcia, L.J., Salazar, G.A., Villaveces, J., Gore, S., Garcia, A., Martin, M.J., Launay, G., Alcantara, R., Del-Toro, N. et al. (2013) BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics, 29, 1103-1104.
10. Sierk, M.L. and Pearson, W.R. (2004) Sensitivity and selectivity in protein structure comparison. Protein Sci., 13, 773-785.
11. Blake, J.A., Dolan, M., Drabkin, H., Hill, D.P., Li, N., Sitnikov, D., Bridges, S., Burgess, S., Buza, T., McCarthy, F. et al. (2013) Gene Ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
12. Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M. et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 41 D456-D463.
13. Smith, B., Ashburner, M., Rosse, C, Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251-1255.
14. Barker, J.A. and Thornton, J.M. (2003) An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics, 19, 1644-1649.