BRENDA in 2017: New perspectives and new tools in BRENDA

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D380-D388

  Placzek, Sandra ^a   Schomburg, Ida ^a   Chang, Antje ^a   Jeske, Lisa ^a   Ulbrich, Marcus ^a   Tillack, Jana ^a   Schomburg, Dietmar ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BRENDA ENZYME DATABASE; COMPUTER ANALYSIS; DATA BASE; ENZYME KINETICS; ENZYME STRUCTURE; INFORMATION PROCESSING; MOLECULAR GENETICS; NOMENCLATURE; PREDICTION; PROTEIN STRUCTURE; SEARCH ENGINE; SEQUENCE ANALYSIS; THREE DIMENSIONAL IMAGING; BIOLOGY; DATA MINING; DRUG DEVELOPMENT; HUMAN; PROCEDURES; PROTEIN DATABASE; SOFTWARE; WEB BROWSER;

ENZYME; LIGAND; PROTEIN BINDING;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, PROTEIN; DRUG DISCOVERY; ENZYMES; HUMANS; LIGANDS; PROTEIN BINDING; SOFTWARE; WEB BROWSER;

EID: 85016103479     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw952     Document Type: Article

References (25)

1. Chang, A., Schomburg, I., Placzek, S., Jeske, L., Ulbrich, M., Xiao, M., Sensen, C.W. and Schomburg, D. (2015) BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res., 43, D439-D446.
2. McDonald, A.G., Boyce, S. and Tipton, K.F. (2009) ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Res., 37, D593-D597.
3. The UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
4. Gremse, M., Chang, A., Schomburg, I., Grote, A., Scheer, M., Ebeling, C. and Schomburg, D. (2011) The BRENDA tissue ontology (BTO): the first all-integrating ontology of all organisms for enzyme source. Nucleic Acids Res., 39, D507-D513.
5. Barthelmes, J., Ebeling, C., Chang, A., Schomburg, I. and Schomburg, D. (2007) BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res., 35, D511-D514.
6. NCBI Resource Coordinators. (2014) Database resources of the national center for biotechnology information. Nucleic Acids Res., 42, D7-D17.
7. The Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res. 43, D1049-D1056.
8. Federhen, S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136-D143.
9. Söhngen, C., Chang, A. and Schomburg, D. (2011) Development of a classification scheme for disease-related enzyme information. BMC Bioinformatics, 12, 329.
10. Schomburg, I., Chang, A., Placzek, S., Söhngen, C., Rother, M., Lang, M., Munaretto, C., Ulas, S., Stelzer, M., Grote, A. et al. (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res., 41, D764-D772.
11. Rose, P.W., Prlić, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J.D., Woo, J. et al. (2015) The RCSB protein data bank: views of structural biology for basic and applied research and education. Nucleic Acids Res., 41, D345-D356.
12. Turinsky, A.L., Fanea, E., Trinh, Q., Wat, S., Hallgrímsson, B., Dong, X., Shu, X., Stromer, J.N., Hill, J.W., Edwards, C. et al. (2008) CAVEman: standardized anatomical context for biomedical data mapping. Anat. Sci. Educ., 1, 10-18.
13. Fox, N.K., Brenner, S.E. and Chandonia, J.M. (2014) SCOPe: structural classification of proteins-extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res., 42, D304-D309.
14. Sillitoe, I., Lewis, T.E., Cuff, A., Das, S., Ashford, P., Dawson, N.L., Furnham, N., Laskowski, R.A., Lee, D., Lees, J.G. et al. (2015) CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res., 43, D376-D381.
15. Roncaglia, P., Martone, M.E., Hill, D.P., Berardini, T.Z., Foulger, R.E., Imam, F.T., Drabkin, H., Mungall, C.J. and Lomax, J. (2013) The gene ontology (GO) cellular component ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J. Biomed. Semantics, 4, 20.
16. Quester, S. and Schomburg, D. (2011) EnzymeDetector: an integrated enzyme function prediction tool and database. BMC Bioinformatics, 12, 376.
17. Lang, M., Stelzer, M. and Schomburg, D. (2011) BKM-react, an integrated biochemical reaction database. BMC Biochem., 12, 42.
18. Shannon, P., Markiel, A., Ozier, O., Baliga, N., Wang, J., Ramage, D., Amina, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 11, 2498-2504.
19. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res., 44, D457-D462
20. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., Holland, T.A., Keseler, I.M., Kothari, A., Kubo, A. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471
21. Bannert, C., Welfle, A., aus dem Spring, C. and Schomburg, D. (2010) BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation. BMC Bioinformatics, 11, 589.
22. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 21, 403-410.
23. Gillespie, J.J., Wattam, A.R., Cammer, S.A., Gabbard, J.L., Shukla, M.P., Dalay, O., Driscoll, T., Hix, D., Mane, S.P., Mao, C. et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect. Immun., 79, 4286-4298.
24. Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A. et al. (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res., 44, D279-D285.
25. Finn, R.D., Clements, J., Arndt, W., Miller, B.L., Wheeler, T.J., Schreiber, F., Bateman, A. and Eddy, S.R. (2015) HMMER web server: 2015 update. Nucleic Acids Res., 43, W30-W38.