LIGAND: Chemical database for enzyme reactions

Bioinformatics

Volumn 14, Issue 7, 1998, Pages 591-599

  Goto, Susumu ^a   Nishioka, Takaaki ^b   Kanehisa, Minoru ^a  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUND; ENZYME;

ARTICLE; BIOLOGY; CHEMICAL REACTION; CHEMICAL STRUCTURE; DATA BASE; ENZYME MECHANISM; INFORMATION SCIENCE; INTERNET; METABOLISM; NOMENCLATURE; PRIORITY JOURNAL;

EID: 0031715499     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.7.591     Document Type: Article

References (32)

1. Bairoch, A. (1996) The ENZYME data bank in 1995. Nucleic Acids Res., 24, 221-222.
2. Bairoch, A. and Apweiler, R. (1997) The SWISS-PROT protein sequence data bank and its supplment TrEMBL. Nucleic Acids Res., 25, 31-36.
3. Bairoch, A., Bucher, P. and Hofmann, K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res., 25, 217-221.
4. Benson, D.A., Boguski, M.S., Lipman, D. and Ostell, J. (1997) Gen-Bank. Nucleic Acids Res., 25, 1-6.
5. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) The protein data bank: A computer-based archival file for macromolecular structures. J Mol. Biol., 112, 535-542.
6. Bono, H., Ogata, H., Goto, S. and Kanehisa, M. (1998) Prediction of enzyme genes in complete genomes by reconstruction of metabolic pathways. Genome Res., 8, 203-210.
7. Budavari, S. (ed.) (1996) The MERCK Index, 12th edn. Merck & Co., Inc., Whitehouse Station.
8. Ellis, L.B.M. and Wackett, L.P. (1995) A microbial biocatalysis database. Soc. Ind. Microbiol. News, 45, 167-173.
9. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y. and Kanesa, M. (1998) DBGET/LinkDB: an integrated database retrieval system. In Altman, R.B., Dunker, A.K., Hunter, L. and Klein, T.E. (eds), Pacific Symposium on Biocomputing '98. World Scientific, Maui, pp. 683-694.
10. Gaasterland, T., Godfrey, P. and Minker, J. (1992) An overview of cooperative answering. J. Intell. Inf. Syst., 1, 123-157.
11. George, D.G. et al. (1997) The protein information resource (PIR) and the PIR-international protein sequence database. Nucleic Acids Res., 25, 24-27.
12. Gerhard, M. (ed.) (1992) Biological Pathways, 3rd edn. Boehringer Mannheim, Mannheim.
13. Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K. and Kanehisa, M. (1997) Organizing and computing metabolic pathway data in terms of binary relations. In Altman, R.B., Dunker, A.K., Hunter, L. and Klein, T.E. (eds), Pacific Symposium on Biocomputing '97. World Scientific, Maui, pp. 175-186.
14. Hofestädt, R. and Meineke, F. (1995) Interactive modelling and simulation of biochemical networks. Comput. Biol. Med., 25, 321-334.
15. Hubbard, T.J.P., Murzin, A.G., Brenner, S.E. and Chothia, C. (1997) SCOP: a Structural Classification of Proteins database. Nucleic Acids Res., 25, 236-239.
16. IUBMB (1992) Enzyme Nomenclature: Recommendations (1992) of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Academic Press, New York.
17. Kanehisa, M. (1997a) Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem. Sci., 22, 442-444.
18. Kanehisa, M. (1997b) A database for post-genome analysis. Trends Genet., 13, 375-376.
19. Karp, P.D. (1992) A knowledge base of the chemical compounds of intermediary metabolism. Comput. Applic. Biosci., 8, 347-357.
20. Karp, P.D., Ouzounis, C. and Paley, S. (1996) Hin-Cyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae. In Proceedings of Intelligent Systems for Molecular Biology '96, AAAI Press, Menlo Park, pp. 116-124.
21. Karp, P.D., Riley, M., Paley, S.M., Pelligrini-Toole, A. and Krummenacker, M. (1997) EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res., 25, 43-50.
22. Kazic, T. (1993) Reasoning about biochemical compounds and processes. In Proceedings of Second International Conference on Bioinformatics, Super-computing and the Human Genome Project, pp. 35-49.
23. Mavrovouniotis, M.L. (1993) Identification of qualitatively feasible metabolic pathways. In Hunter, L. (ed.), Artificial Intelligence and Molecular Biology. AAAI Press, Menlo Park, pp. 325-364.
24. Nishioka, T., Sumi, K. and Oda, J. (1989) Finding lead structures from amino acid sequence similarities of target proteins. In Magee, P.S., Henry, D.R. and Block, J.H. (eds), Probing Bioactive Mechanism. American Chemical Society, New York, pp. 105-122.
25. Ochs, R.S., Qureschi, A., Sycz, A. and Vorbach, J. (1995) A computerized metabolic map. 2. relational structure, extended modeling and a graphical interface. J. Chem. Inf. Comput. Sci., 36, 594-601.
26. Ogata, H., Bono, H., Fujibuchi, W., Goto, S. and Kanehisa, M. (1996) Analysis of binary relations and hierarchies of enzymes in the metabolic pathways. In Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S. and Nakai, K. (eds), Genome Informatics 1996. Universal Academy Press, Tokyo, pp. 128-136.
27. Pearson, P., Francomano, C., Foster, P., Bocchini, C., Li, P. and McKusick, V. (1994) The status of online Mendelian inheritance in man (OMIM) medio 1994. Nucleic Acids Res., 22, 3470-3473.
28. Schomburg, D. (ed.) (1990) Enzyme Handbook 1-12. Springer-Verlag, Heidelberg.
29. Seikov, E. et al. (1997) The metabolic pathway collection: an update. Nucleic Acids Res., 25, 37-38.
30. Stoesser, G., Strek, P., Tuli ,M.A., Stoehr, P.J. and Cameron, G.N. (1997) The EMBL nucleotide sequence database. Nucleic Acids Res., 25, 7-14.
31. Sumi, K., Nishioka, T. and Oda, J. (1991) Similarity graphing and enzyme-reaction database: methods to detect sequence regions of importance for recognition of chemical structures. Protein Eng., 4, 413-420.
32. Suyama, M., Ogiwara, A., Nishioka, T. and Oda, J. (1993) Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database. Comput. Applic. Biosci., 9, 9-15.