Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions

Journal of the American Chemical Society

Volumn 126, Issue 50, 2004, Pages 16487-16498

  Kotera, Masaaki ^a   Okuno, Yasushi ^a   Hattori, Masahiro ^a   Goto, Susumu ^a   Kanehisa, Minoru ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; METABOLISM; PROTEINS;

ENZYME COMMISSION (EC); GENOMIC-SCALE ANALYSIS; METABOLIC RECONSTRUCTION;

ENZYME KINETICS;

ACCURACY; ARTICLE; CLUSTER ANALYSIS; CORRELATION ANALYSIS; DECOMPOSITION; ENZYME MECHANISM; GENETIC ANALYSIS; GENOME; GENOMICS; MATHEMATICAL COMPUTING; METABOLISM; STRUCTURE ANALYSIS; VALIDATION PROCESS;

COMPUTERS; ENZYMES; GENOME; STRUCTURE-ACTIVITY RELATIONSHIP; TERMINOLOGY;

EID: 11444249446     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0466457     Document Type: Article

References (20)

1. Kanehisa, M.; Bork, P. Bioinformatics in the post-sequence era. Nat. Genet. 2003, 33, 305-310.
2. Kanehisa, M. A database for post-genome analysis. Trends Genet. 1997, 13, 375-376.
3. Kanehisa, M.; Goto, S.; Kawashima, S.; Okuno, Y.; Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004, 32, D277-D280.
4. Barrett, A. J.; Canter, C. R.; Liebecq, C.; Moss, G. P.; Saenger, W.; Sharon, N.; Tipton, K. F.; Vnetianer, P.; Vliegenthart, V. F. G. Enzyme Nomenclature; Academic Press: San Diego, CA, 1992.
5. Hattori, M.; Okuno, Y.; Goto, S.; Kanehisa, M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 2003, 125, 11853-11865.
6. Goto, S.; Nishioka, T.; Kanehisa, M. LIGAND: chemical database for enzyme reactions. Bioinformatics 1998, 14, 591-599.
7. Flower, D. R. On the properties of bit string-based measures of chemical similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.
8. Qu, D. L.; Fu, B.; Muraki, M.; Hayakawa, T. An encoding system for a group contribution method. J. Chem. Inf. Comput. Sci. 1992, 32, 443-447.
9. Arita, M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 2003, 13, 2455-2466.
10. Cai, C. Z.; Han, L. Y.; Ji, Z. L.; Chen, Y. Z. Enzyme family classification by support vector machines. Proteins 2004, 55, 66-76.
11. Babbitt, P. C. Definitions of enzyme function for the structural genomics era. Curr. Opin. Chem. Biol. 2003, 7, 230-237.
12. Shakhnovich, B. E.; Max Harvey, J. Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation. J. Mol. Biol. 2004, 337, 933-949.
13. Devos, D.; Valencia, A. Practical limits of function prediction. Proteins 2000, 41, 98-107.
14. Orengo, C. A.; Pearl, F. M.; Bray, J. E.; Todd, A. E.; Martin, A. C.; Lo Conte, L.; Thornton, J. M. The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res. 1999, 27, 275-279.
15. Todd, A. E.; Orengo, C. A.; Thornton, J. M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 2001, 307, 1113-1143.
16. Hegyi, H.; Gerstein, M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 1999, 288, 147-164.
17. Ma, H.; Zeng, A. P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19, 270-277.
18. Goesmann, A.; Haubrock, M.; Meyer, F.; Kalinowski, J.; Giegerich, R. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics 2002, 18, 124-129.
19. Bono, H.; Ogata, H.; Goto, S.; Kanehisa, M. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 1998, 8, 203-210.
20. Coutinho, P. M.; Deleury, E.; Davies, G. J.; Henrissat, B. An evolving hierarchical family classification for glycosyltransferases. J. Mol. Biol. 2003, 328, 307-317.