E-zyme: Predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs

Bioinformatics

Volumn 25, Issue 12, 2009, Pages

  Yamanishi, Yoshihiro ^a,c   Hattori, Masahiro ^a   Kotera, Masaaki ^a   Goto, Susumu ^a   Kanehisa, Minoru ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; BIOTRANSFORMATION; COMPUTER PREDICTION; CONFERENCE PAPER; CONTROLLED STUDY; ENZYME MECHANISM; ENZYME SUBSTRATE; INTERMETHOD COMPARISON; METABOLOMICS; ONLINE SYSTEM; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; ENZYMES; INTERNET; SOFTWARE; SUBSTRATE SPECIFICITY;

EID: 66349127228     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp223     Document Type: Conference Paper

References (21)

1. Barrett, A. J. et al. (1992) Enzyme Nomenclature. Academic Press, San Diego, California.
2. Darvas, F. (1988) Predicting metabolic pathways by logic programming. J. Mol. Graphis, 6, 80-86.
3. Dobson, C. M. (2004) Chemical space and biology. Nature, 432 824-828.
4. Ellis, L. B. M. et al. (2006) The university of minnesota biocatalysis/biodegradation database: The first decade. Nucleic Acids Res., 34, D517-D521.
5. Hattori, M. et al. (2003) Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc., 125 11853-11865.
6. Hou, B. K. et al. (2004) Encoding microbial metabolic logic: predicting biodegradation. J. Ind. Microbiol. Biotechnol., 31 261-272.
7. Kanehisa, M. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
8. Kanehisa, M. et al. From genomics to chemical genomics: New developments in KEGG (2006) Nucleic Acids Res., 34, D354-D357.
9. Klopman, G. and Tu, M. (1997) Structure-biodegradability study and computer-automated prediction of aerobic biodegradation of chemicals. Environ. Toxicol. Chem., 16, 1829-1835.
10. Kotera, M. et al. (2008) Eliciting possible reaction equations and metabolic pathways involving orphan metabolites. J. Chem. Inf. Model. 48, 2335-2349.
11. Kotera, M. et al. (2004) Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc., 126, 16487-16498.
12. Langowski, J. and Long, A. (2002) Computer systems for the prediction of xenobiotic metabolism. Advanced Drug Delivery Reviews, 54, 407-415.
13. Latino, D.A. et al. (2008) Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps. Bioinformatics, 24, 2236-2244.
14. Mayeno, A. N. et al. (2005) Biochemical reactions network modeling: Predicting metabolism of organic chemical mixtures. Environ. Sci. Technol., 39, 5363-5371.
15. McShan, D. C. et al. (2004) Symbolic inference of xenobiotics metabolism. Pac. Symp. Biocomput, 9, 545-556.
16. Nobeli, I. and Thornton, J. M. (2006) A bioinformatician's view of the metabolome. BioEssays, 28, 534-545.
17. Oh, M. et al. (2007) Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf. Model., 47, 1702-1712.
18. Stockwell, B. R. (2000) Chemical genetics: Ligand-based discovery of gene function. Nat. Rev. Genet., 1, 116-125.
19. Talafous, J. et al. (1994) META. 2. A dictionary model of mammalian xenobiotic metabolism. J. Chem. Inf. Comput. Sci., 34 1326-1333.
20. Tipton, K. F. and Boyce, S. (2000) History of the enzyme nomenclature system. Bioinformatics, 16, 34-40.
21. Zhang, Q.Y. and Aires-de-Sousa, J. (2005) Structure-based classification of chemical reactions without assignment of reaction. J. Chem. Inf. Model., 45, 1775-1783.