Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways

Journal of the American Chemical Society

Volumn 125, Issue 39, 2003, Pages 11853-11865

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

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR INTERACTIONS;

ALGORITHMS; HEURISTIC METHODS; METABOLISM; MOLECULAR ORIENTATION; NUCLEIC ACIDS; STRUCTURE (COMPOSITION);

PROTEINS;

CARBOHYDRATE; CARBON; NITROGEN; NUCLEIC ACID; OXYGEN; PROTEIN;

ALGORITHM; ARTICLE; CELL FUNCTION; CHEMICAL STRUCTURE; GENE STRUCTURE; GENOMICS; METABOLISM; MOLECULAR INTERACTION; OPERON;

ALGORITHMS; GENOME; METABOLISM; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MODELS, GENETIC; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0141843591     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja036030u     Document Type: Article

References (47)

1. Kanehisa, M.; Bork, P. Bioinformatics in the post-sequence era. Nat. Genet. 2003, 33. 305-310.
2. Eisenberg, D.; Marcotte, E. M.; Xenarios, I.; Yeates, T. O. Protein function in the post-genomic era. Nature 2000, 405, 823-826.
3. Kanehisa, M. Prediction of higher order functional networks from genomic data, Pharmacogenomics 2001, 2, 373-385.
4. Velculescu, V. E.; Zhang, L.; Zhou, W,; Vogelstein, J.; Basrai, M. A.; Bassett, D. E., Jr.; Hieter, P.; Vogelstein, B.; Kinzler, K, W. Characterization of the yeast transcriptome. Cell 1997, 88, 243-251.
5. Wilkins, M. R.; Sanchez, J. C.; Gooley, A. A.; Appel, R. D.; Humphery-Smith, I.; Hochstrasser, D. F.; Williams, K, L. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev. 1996, 13, 19-50.
6. Tweeddale, H.: Notley-McRobb, L.; Ferenci, T. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis. J. Bacteriol. 1998, 180. 5109-5116.
7. Kanehisa, M. A database for post-genome analysis. Trends Genet. 1997, 13, 375-376.
8. Kanehisa, M.; Goto, S.; Kawashima, S.; Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 2002, 30, 42-46.
9. Schulze-Kremer, S. Ontologies for molecular biology. Pac. Symp. Biocomput. 1998, 3, 693-704.
10. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.: Hill, D. P.: Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
11. Tatusov, R. L.; Koonin, E. V.; Lipman, D. J. A genomic perspective on protein families. Science 1997, 278, 631-637.
12. Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247, 536-540.
13. Conte, L. L.; Brenner, S. E.; Hubbard, T. J. P.; Chothia, C.; Murzin, A. G. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res. 2002, 30, 264-267.
14. Orengo, C. A.; Michie, A. D.; Jones, S.: Jones, D. T.; Swindells, M. B.; Thornton, J. M. CATH: A hierarchic classification of protein domain structures. Structure 1997, 5, 1093-1108.
15. Flower, D. R. On the properties of bit string-based measures of chemical similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.
16. Allen, F. H.; Kennard, O. 3D search and research using the Cambridge structural database. Chem. Des. Autom. News 1993, 8, 1 and 31-37.
17. Brown, R. D.; Martin, Y. C. Use of structure -activity data to compare structure-based clustering methods and descriptors for use in compound selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
18. Brown, R. D.; Martin, Y. C. The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 1997, 37, 1-9.
19. James, C. A.; Weininger, D.; Delany, J. Daylight Theory Manual 4.71; Daylight Chemical Information Systems, Inc.: Irvine. CA, 2000.
20. Willett, P. Searching for pharmacophoric patterns in databases of three-dimensional chemical structures. J. Mol. Recognit. 1995, 8, 290-303.
21. Miller, M. A. Chemical database techniques in drug discovery. Nat. Rev. Drug Discovery 2002, 220, 220-227.
22. Arita, M. Graph modeling of metabolism. J. Jpn. Soc. A. 1. 2000, 15, 703-710.
23. Weininger, D. SMILES 1. Introduction and Encoding Rules. ¿ Chem. Inf. Comput. Sci. 1988, 28, 31-36.
24. 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.
25. Raymond, J. W.; Willett, P. Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J. Comput.-Aided Mol. Des. 2002. 16, 521-533.
26. Raymond, J. W.; Gardiner, E. J.; Willett, P. RASCAL: Calculation of graph similarity using maximum common edge subgraphs. Comput. J. 2002, 45, 631-644.
27. Raymond, J. W.; Gardiner, E. J.; Willett, P. Heuristics for similarity searching of chemical graphs using a maximum common edge subgraph algorithm. J. Chem. Inf. Comput. Sci. 2002, 42, 305-316.
28. Mavrovouniotis, M. L. Group contributions for estimation standard Gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol. Bioeng. 1990, 36, 1070-1082.
29. Mavrovouniotis, M. L. Estimation of standard Gibbs energy changes of biotransformations. J. Biol. Chem. 1991, 266, 14440-14445.
30. Forsythe, R. G., Jr.; Karp, P. D.; Mavrovouniotis, M. L. Estimation of equilibrium constants using automated group contribution methods. Comput. Appl. Biosci. 1997, 13, 537-543.
31. Fujibuchi, W.; Ogata, H.; Matsuda, H.; Kanehisa, M. Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res. 2000, 28, 4029-4036.
32. Goto, S.; Nishioka, T.; Kanehisa, M. LIGAND: chemical database for enzyme reactions. Bioinformatics 1998, 14, 591-599.
33. Goto, S.; Okuno, Y.; Hattori, M.; Nishioka, T.; Kanehisa, M. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 2002, 30, 402-404.
34. Kuhl, F. S.; Crippen, G. M.; Friesen, D. K. A combinatorial algorithm for calculating ligand binding. J. Comput. Chem. 1984, 5, 24-34.
35. Takahashi, Y.; Maeda, S.; Sasaki, S. Automated recognition of common geometrical patterns among a variety of three-dimensional molecular stuctures. Anal. Chim. Acta 1987, 200, 363-377.
36. Bron, C.; Kerbosch, J. Algorithm 457: Finding all cliques of an undirected graph. Commun. ACM 1973, 16, 575-577.
37. Jaccard, P. The distribution of the flora of the alpine zone. New Phytol. 1912, 11, 37-50.
38. Watson, G. A. An algorithm for the single facility location problem using the Jaccard metric. SIAM J. Sci. Stat. Comput. 1983, 4, 748-756.
39. Willett, P.; Winterman, V.; Bawden, D. Implementation of nearest-neighbor searching in an online chemical structure search system. J. Chem. Inf. Comput. Sci. 1986, 26, 36-41.
40. Willett, P.; Barnard, J.; Downs, G. M. Chemical similarity searching. J. Chem. Inf. Comput. Sci. 1998, 38. 983-996.
41. Barabasi, A. L.; Albert, R. Emergence of scaling in random networks. Science 1999, 286, 509-512.
42. Ogata, H.: Fujibuchi, W.; Goto, S.; Kanehisa, M. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 2000, 28, 4021-4028.
43. Parkhill, J.; Wren, B. W.; Thomson, N. R.; Titball, R. W.; Holden, M. T. ; Prentice, M. B.; Sebaihia, M.; James, K. D.; Churcher, C.; Mungall, K. L.; Baker, S.; Basham, D.; Bentley, S. D.; Brooks, K.: Cerdeno-Tarraga, A. M.; Chillingworth, T.; Cronin, A.; Davies, R. M.; Davis, P.; Dougan, G.; Feltwell, T.; Hamlin, N.; Holroyd, S.; Jagels, K.; Karlyshev, A. V.; Leather, S.; Moule, S.; Oyston, P. C.; Quail, M.; Rutherford, K.; Simmonds. M.; Skelton, J.; Stevens, K.; Whitehead, S.; Barrell, B. G. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 2001, 413, 523-527.
44. DelVecchio, V. G.; Kapatral, V.; Redkar, R. J.; Patra, G.; Mujer, C.; Los, T.; Ivanova, N.; Anderson, I.; Bhattacharyya, A.; Lykidis, A.; Reznik, G.; Jablonski, L.; Larsen, N.; D'Souza, M.; Bemal, A.; Mazur, M.; Goltsman, E.; Selkov, E.; Elzer, P. H.; Hagius, S.; O'Callaghan, D.; Letesson, J. J.; Haselkom, R,; Kyrpides, N.; Overbeek, R. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 443-448.
45. Kunst, F.; Ogasawara, N.; Moszer, I.; Albertini, A. M.; Alloni, G.; Azevedo, V.; Bertero, M. G.; Bessieres. P.; Bolotin, A.; Borchert, S.; Borriss, R.; Boursier, L.; Brans, A.; Braun, M.; Brignell, S. C.; Bron, S.; Brouillet, S.; Bruschi, C. V.; Caldwell, B.; Capuano, V,; Carter, N. M.; Choi, S. K.; Codani, J. J.; Connerton, I. F.; Cummings, N. J.; Daniel, R. A,; Denizot, F.; Devine, K. M.; Dusterhoft, A.; Ehrlich, S. D.; Emmerson, P. T.; Entian, K. D.; Errington, J.; Fabret, C.; Ferrari, E.; Foulger, D.; Fritz, C.; Fujita, M,; Fujita, Y.; Fuma, S.; Galizzi, A.; Galleron, N.; Ghim, S. Y.; Glaser, P.; Goffeau, A.; Golightly, E. J.; Grandi, G.; Guiseppi, G.; Guy, B. J.; Haga, K.; Haiech, J.; Harwood: C. R.; Henaut, A.; Hilbert, H.; Holsappel, S.: Hosono, S.; Hullo, M. F.; Itaya, M.; Jones, L.; Joris, B.; Karamata, D.; Kasahara, Y.; Klaerr-Blanchard, M.; Klein, C.; Kobayashi, Y.; Koetter, P.; Koningstein, G.; Krogh, S.; Kumano, M.; Kurita, K.; Lapidus, A.; Lardinois, S,; Lauber, J.; Lazarevic, V.; Lee, S. M.; Levine, A.; Liu, H.; Masuda, S.; Mauel, C.; Medigue, C.; Medina, N.; Mellado, R. P.; Mizuno, M.; Moestl, D.; Nakai, S.; Noback, M.; Noone, D.; O'Reilly, M.; Ogawa, K.; Ogiwara, A.; Oudega, B.; Park, S. H.; Parro, V.; Pohl, T. M.; Poetetelle, D.; Porwollik, S.; Prescott, A. M.; Presecan, E.; Pujic, P.; Pumelle, B.; Rapoport, G.; Rey, M.; Reynolds, S.; Rieger, M.; Rivolta, C.; Rocha, E.; Roche, B.; Rose, M.; Sadaie, Y.; Sato, T.; Scanlan, E.; Schleich, S.; Schroeter, R.; Scoffone, F.; Sekiguchi, J.; Sekowska, A.; Seror, S. J.; Serror, P.; Shin, B. S.; Soldo, B.; Sorokin, A.; Tacconi, E.; Takagi, T. ; Takahashi, H.; Takemaru, K.; Takeuchi, M.; Tamakoshi, A.; Tanaka, T.; Terpstra, P.; Tognoni, A.; Tosato, V.; Uchiyama, S.; Vandenbol, M.; Vannier, F. ; Vassarotti, A.; Viari, A.: Wambutt, R.; Wedler, E.; Wedler, H.; Weitzenegger, T.; Winters, P.; Wipat, A.; Yamamoto, H.; Yamane, K.; Yasumoto, K.; Yata, K.; Yoshida, K.; Yoshikawa, H. F.; Zumstein, E.; Yoshikawa, H.; Danchin, A. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 1997, 390, 249-256.
46. Blattner, F. R.; Plunkett, G., 3rd; Bloch, C. A.; Perna, N. T.; Burland, V.; Riley, M.; Collado-Vides, J.; Glasner, J. D.; Rode, C. K.; Mayhew, G. F.; Gregor, J.; Davis, N. W.; Kirkpatrick, H. A.; Goeden, M. A.; Rose, D. J.; Mau, B.; Shao, Y. The complete genome sequence of Escherichia coli K- 12. Science 1997, 277, 1453-1474.
47. Parkhill, J.; Dougan, G.; James, K. D.; Thomson, N. R.; Pickard, D.; Wain, J.; Churcher, C.; Mungall, K. L.; Bentley, S. D.; Holden, M. T.; Sebaihia, M.; Baker, S.; Basham, D.; Brooks, K.; Chillingworth, T.; Connerton, P.; Cronin, A.; Davis, P.; Davies, R. M.; Dowd, L.; White, N.; Farrar, J.; Feltwell, T.; Hamlin, N.; Haque, A.; Hien, T. T.; Holroyd, S.; Jagels, K.; Krogh, A.; Larsen, T. S.; Leather, S.; Moule, S.; O'Gaora, P.; Parry, C.; Quail, M.; Rutherford, K.; Simmonds, M.; Skelton, J.; Stevens, K.; Whitehead, S.; Barrell, B. G. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001, 413, 848-852