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Volumn 18, Issue 1, 2011, Pages 43-58

Computing atom mappings for biochemical reactions without subgraph isomorphism

Author keywords

algorithms; biochemical networks

Indexed keywords

AMINO ACID;

EID: 78651301358     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0216     Document Type: Article
Times cited : (26)

References (53)
  • 1
    • 3142626457 scopus 로고    scopus 로고
    • Efficient extraction of mapping rules of atoms from enzymatic reaction data
    • Akutsu, T. 2004. Efficient extraction of mapping rules of atoms from enzymatic reaction data. J. Comput. Biol. 11, 449-462.
    • (2004) J. Comput. Biol. , vol.11 , pp. 449-462
    • Akutsu, T.1
  • 2
    • 0012074826 scopus 로고    scopus 로고
    • Graph modeling of metabolism
    • Arita, M. 2000. Graph modeling of metabolism. J. Jpn. Soc. Artif. Intell. 15, 703-710.
    • (2000) J. Jpn. Soc. Artif. Intell. , vol.15 , pp. 703-710
    • Arita, M.1
  • 3
    • 0242574984 scopus 로고    scopus 로고
    • In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism
    • Arita, M. 2003. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 13, 2455-2466.
    • (2003) Genome Res. , vol.13 , pp. 2455-2466
    • Arita, M.1
  • 4
    • 78651327384 scopus 로고    scopus 로고
    • Introduction to the arm database: Database on chemical transformation in metabolism for tracing pathways
    • Springer, Tokyo.
    • Arita, M. 2005. Introduction to the arm database: database on chemical transformation in metabolism for tracing pathways, 193-210. In: Metabolomics, The Frontier of Systems Biology. Volume 4. Springer, Tokyo.
    • (2005) Metabolomics the Frontier of Systems Biology , vol.4 , pp. 193-210
    • Arita, M.1
  • 5
    • 78651286363 scopus 로고    scopus 로고
    • Topological indices in combinatorial chemistry 419-463
    • John Wiley & Sons, Inc., New York.
    • Bereg, S. 2008. Topological indices in combinatorial chemistry, 419-463. In: Bioinformatics Algorithms: Techniques and Applications. John Wiley & Sons, Inc., New York.
    • (2008) Bioinformatics Algorithms: Techniques and Applications
    • Bereg, S.1
  • 6
    • 0037393779 scopus 로고    scopus 로고
    • Bond dissociation energies of organic molecules
    • Blanskby, S., and Ellison, G. 2003. Bond dissociation energies of organic molecules. Acc. Chem. Res. 36, 255-263.
    • (2003) Acc. Chem. Res. , vol.36 , pp. 255-263
    • Blanskby, S.1    Ellison, G.2
  • 7
    • 47549099578 scopus 로고    scopus 로고
    • Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks
    • Blum, T., and Kohlbacher, O. 2008. Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. J. Comput. Biol. 15, 565-576.
    • (2008) J. Comput. Biol. , vol.15 , pp. 565-576
    • Blum, T.1    Kohlbacher, O.2
  • 8
    • 84976668743 scopus 로고
    • Finding all cliques of an undirected graph
    • ACM
    • Bron, C., and Kerbosch, J. 1971. Finding all cliques of an undirected graph. Commun. ACM 16, 575-577.
    • (1971) Commun. , vol.16 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 9
    • 23844449054 scopus 로고    scopus 로고
    • Graph matching: Theoretical foundations algorithms and applications
    • Bunke, H. 2000. Graph matching: theoretical foundations, algorithms, and applications. Proc. Vision Interface 82-88.
    • (2000) Proc. Vision Interface , pp. 82-88
    • Bunke, H.1
  • 10
    • 27844520909 scopus 로고    scopus 로고
    • An algorithm for reporting maximal c-cliques
    • Cazals, F., and Karande, C. 2005. An algorithm for reporting maximal c-cliques. Theor. Comput. Sci. 349, 484-490.
    • (2005) Theor. Comput. Sci. , vol.349 , pp. 484-490
    • Cazals, F.1    Karande, C.2
  • 11
    • 53249115253 scopus 로고    scopus 로고
    • A note on the problem of reporting maximal cliques
    • Cazals, F., and Karande, C. 2008. A note on the problem of reporting maximal cliques. Theor. Comput. Sci. 407, 564-568.
    • (2008) Theor. Comput. Sci. , vol.407 , pp. 564-568
    • Cazals, F.1    Karande, C.2
  • 12
    • 0000253451 scopus 로고
    • Molecular structure comparison program for the identification of maximal common substructures
    • Cone, M., Venkataraghaven, R., and McLafferty, F. 1977. Molecular structure comparison program for the identification of maximal common substructures. J. Am. Chem. Soc. 99, 7668-7671.
    • (1977) J. Am. Chem. Soc. , vol.99 , pp. 7668-7671
    • Cone, M.1    Venkataraghaven, R.2    McLafferty, F.3
  • 14
    • 84890410415 scopus 로고    scopus 로고
    • Performance evaluation of the vf graph matching algorithm
    • Cordella, L.P., Foggia, P., Sansone, C., et al. 1999. Performance evaluation of the vf graph matching algorithm. Proc. ICIAP-99 1172.
    • (1999) Proc. ICIAP , vol.99 , pp. 1172
    • Cordella, L.P.1    Foggia, P.2    Sansone, C.3
  • 16
    • 17444411955 scopus 로고    scopus 로고
    • Cytochrome p450 in silico: An integrative modeling approach
    • de Graaf, C., Vermeulen, N.P.E., and Feenstra, K.A. 2005. Cytochrome p450 in silico: an integrative modeling approach. J. Med. Chem. 48, 2725-2755.
    • (2005) J. Med. Chem. , vol.48 , pp. 2725-2755
    • De Graaf, C.1    Vermeulen, N.P.E.2    Feenstra, K.A.3
  • 17
    • 0022094206 scopus 로고
    • Generalized best-first search strategies and the optimality of A*
    • Dechter, R., and Pearl, J. 1985. Generalized best-first search strategies and the optimality of A*. J. ACM 32, 505-536.
    • (1985) J. ACM , vol.32 , pp. 505-536
    • Dechter, R.1    Pearl, J.2
  • 18
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • USA
    • Duarte, N.C., Becker, S.A., Jamshidi, N., et al. 2007. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Nat. Acad. Sci. USA 104.
    • (2007) Proc. Nat. Acad. Sci. , vol.104
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3
  • 19
    • 33748584863 scopus 로고    scopus 로고
    • Mechanisms and free energies of enzymatic reactions
    • Gao, J., Ma, S., Major, D.T., et al. 2006. Mechanisms and free energies of enzymatic reactions. Chem. Rev. 106, 3188-3209.
    • (2006) Chem. Rev. , vol.106 , pp. 3188-3209
    • Gao, J.1    Ma, S.2    Major, D.T.3
  • 20
    • 38249033005 scopus 로고
    • Allylglucosinolate biosynthesis in brassica carinata
    • Glover, J.R., Chapple, C.C.S., Rothwell, S., et al. 1988. Allylglucosinolate biosynthesis in Brassica carinata. Phytochemistry 27, 1345-1348.
    • (1988) Phytochemistry , vol.27 , pp. 1345-1348
    • Glover, J.R.1    Chapple, C.C.S.2    Rothwell, S.3
  • 21
    • 0036081122 scopus 로고    scopus 로고
    • Ligand: A database of chemical compounds and reactions in biological pathways
    • Goto, S., Okuno, Y., Hattori, M., et al. 2002. LIGAND: a database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 402-404
    • Goto, S.1    Okuno, Y.2    Hattori, M.3
  • 22
    • 84899829959 scopus 로고
    • A formal basis for the heuristic determination of minimum cost paths
    • Hart, P.E., Nilsson, N.J., and Raphael, B. 1968. A formal basis for the heuristic determination of minimum cost paths. IEEE Trans. Syst. Sci. Cybernet. 4, 100-107.
    • (1968) IEEE Trans. Syst. Sci. Cybernet. , vol.4 , pp. 100-107
    • Hart, P.E.1    Nilsson, N.J.2    Raphael, B.3
  • 23
    • 14944357243 scopus 로고    scopus 로고
    • Heuristics for chemical compound matching
    • Hattori, M., Okuno, Y., Goto, S., et al. 2003a. Heuristics for chemical compound matching. Genome Inform. 14, 144-153.
    • (2003) Genome Inform. , vol.14 , pp. 144-153
    • Hattori, M.1    Okuno, Y.2    Goto, S.3
  • 24
    • 0141843591 scopus 로고    scopus 로고
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    • Hattori, M., Okuno, Y., Goto, S., et al. 2003b. 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.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 11853-11865
    • Hattori, M.1    Okuno, Y.2    Goto, S.3
  • 25
    • 59349107721 scopus 로고    scopus 로고
    • Analysis of metabolic network based on conservation of molecular structure
    • Hogiri, T., Furusawa, C., Shinfuku, Y., et al. 2008. Analysis of metabolic network based on conservation of molecular structure. BioSystems 95, 175-178.
    • (2008) BioSystems , vol.95 , pp. 175-178
    • Hogiri, T.1    Furusawa, C.2    Shinfuku, Y.3
  • 26
    • 0033982936 scopus 로고    scopus 로고
    • Kegg: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M., and Goto, S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 27
    • 33644874819 scopus 로고    scopus 로고
    • From genomics to chemical genomics: New developments in kegg
    • Kanehisa, M., Goto, S., Hattori, M., et al. 2006. From genomics to chemical genomics: new developments in kegg. Nucleic Acids Res. 34, 354-357.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 354-357
    • Kanehisa, M.1    Goto, S.2    Hattori, M.3
  • 28
    • 6944256505 scopus 로고    scopus 로고
    • The E coli ecocyc database: No longer just a metabolic pathway database
    • Karp, P.D., Arnaud, M., Collado-Vides, J., et al. 2004. The E. coli EcoCyc Database: no longer just a metabolic pathway database. ASM News 70, 25-30.
    • (2004) ASM News , vol.70 , pp. 25-30
    • Karp, P.D.1    Arnaud, M.2    Collado-Vides, J.3
  • 29
    • 2942676743 scopus 로고    scopus 로고
    • Metabolomics and systems biology: Making sense of the soup
    • Kell, D. 2004. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296-307.
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 296-307
    • Kell, D.1
  • 30
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano, H. 2002. Systems biology: a brief overview. Science 295, 1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 31
    • 0034909407 scopus 로고    scopus 로고
    • Enumerating all connected maximal common subgraphs in two graphs
    • Koch, I. 2001. Enumerating all connected maximal common subgraphs in two graphs. Theor. Comput. Sci. 250, 1-30.
    • (2001) Theor. Comput. Sci. , vol.250 , pp. 1-30
    • Koch, I.1
  • 32
    • 45249101693 scopus 로고    scopus 로고
    • Rpair: A reactant-pair database representing chemical changes in enzymatic reactions
    • Kotera, M., Hattori, M., Oh, M.A., et al. 2004. Rpair: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Inform. 15, P062.
    • (2004) Genome Inform. , vol.15
    • Kotera, M.1    Hattori, M.2    Oh, M.A.3
  • 33
    • 0004933817 scopus 로고
    • A note on the derivation of maximal common subgraphs of two directed or undirected graphs
    • Levi, G. 1972. A note on the derivation of maximal common subgraphs of two directed or undirected graphs. Calcolo 9, 1-12.
    • (1972) Calcolo. , vol.9 , pp. 1-12
    • Levi, G.1
  • 34
    • 0014285095 scopus 로고
    • Storage and retrieval of information on chemical structures by computer
    • Lynch, M. 1968. Storage and retrieval of information on chemical structures by computer. Endeavour 27, 68-73.
    • (1968) Endeavour , vol.27 , pp. 68-73
    • Lynch, M.1
  • 35
  • 36
    • 0026353854 scopus 로고
    • Estimation of standard Gibbs energy changes of biotransformations
    • Mavrovouniotis, M. 1991. Estimation of standard Gibbs energy changes of biotransformations. J. Biol. Chem. 266, 14440-14445.
    • (1991) J. Biol. Chem. , vol.266 , pp. 14440-14445
    • Mavrovouniotis, M.1
  • 37
    • 0019599369 scopus 로고
    • Use of a maximal common subgraph algorithm in the automatic identification of the ostensible bond changes occurring in chemical reactions
    • McGregor, J., and Willett, P. 1981. Use of a maximal common subgraph algorithm in the automatic identification of the ostensible bond changes occurring in chemical reactions. J. Chem. Inform. Comput. Sci. 21.
    • (1981) J. Chem. Inform. Comput. Sci. , vol.21
    • McGregor, J.1    Willett, P.2
  • 38
    • 67649984571 scopus 로고    scopus 로고
    • Computer aided optimization of carbon atom labeling for tracer experiments
    • Menküc, B., Gille, C., and Holzhü tter, H. 2008. Computer aided optimization of carbon atom labeling for tracer experiments. Genome Inform. 20, 270-276.
    • (2008) Genome Inform. , vol.20 , pp. 270-276
    • Menküc, B.1    Gille, C.2    Holzhütter, H.3
  • 39
    • 36549016573 scopus 로고    scopus 로고
    • Carbon-fate maps for metabolic reactions
    • Mu, F., Williams, R., Unkefer, C., et al. 2007. Carbon-fate maps for metabolic reactions. Bioinformatics 23, 3193-3199.
    • (2007) Bioinformatics , vol.23 , pp. 3193-3199
    • Mu, F.1    Williams, R.2    Unkefer, C.3
  • 40
    • 0002223982 scopus 로고
    • Algorithms for the assignment and transporation problems
    • Munkres, J. 1957. Algorithms for the assignment and transporation problems. J. Soc. Indust. Appl. Math. 5, 32-38.
    • (1957) J. Soc. Indust. Appl. Math. , vol.5 , pp. 32-38
    • Munkres, J.1
  • 42
    • 33646892443 scopus 로고    scopus 로고
    • Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes
    • Rantanen, A., Mielikäinen, T., Rousu, J., et al. 2006. Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinformatics 22, 1198-1206.
    • (2006) Bioinformatics , vol.22 , pp. 1198-1206
    • Rantanen, A.1    Mielikäinen, T.2    Rousu, J.3
  • 43
    • 45749090110 scopus 로고    scopus 로고
    • An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
    • Rantanen, A., Rousu, J., Jouhten, P., et al. 2008. An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. BMC Bioinform. 9, 266-285.
    • (2008) BMC Bioinform. , vol.9 , pp. 266-285
    • Rantanen, A.1    Rousu, J.2    Jouhten, P.3
  • 44
    • 0036663707 scopus 로고    scopus 로고
    • Maximum common subgraph isomorphism algorithms for the matching of chemical structures
    • DOI 10.1023/A:1021271615909
    • Raymond, J., and Willett, P. 2002. Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J. Comput. Aided Mol. Design 16, 521-533. (Pubitemid 36013605)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.7 , pp. 521-533
    • Raymond, J.W.1    Willett, P.2
  • 46
    • 84958617170 scopus 로고    scopus 로고
    • A method for estimating metabolic fluxes from incomplete isotopomer information
    • Rousu, J., Rantanen, A., Maaheimo, H. et al. 2003. A method for estimating metabolic fluxes from incomplete isotopomer information. Lect. Notes Comput. Sci. 2602, 88-103.
    • (2003) Lect. Notes Comput. Sci. , vol.2602 , pp. 88-103
    • Rousu, J.1    Rantanen, A.2    Maaheimo, H.3
  • 47
    • 0041173950 scopus 로고
    • A graph-theoretical algorithm for matching chemical structures
    • Sussenguth, E. 1965. A graph-theoretical algorithm for matching chemical structures. J. Chem. Doc. 5, 36-43.
    • (1965) J. Chem. Doc. , vol.5 , pp. 36-43
    • Sussenguth, E.1
  • 48
    • 0003237425 scopus 로고
    • Graph algorithms in chemical computation 1-20
    • In Christofferson, R., ed. American Chemical Society, Washington, DC.
    • Tarjan, R. 1977. Graph algorithms in chemical computation, 1-20. In Christofferson, R., ed. lgorithms for Chemical Computations. American Chemical Society, Washington, DC.
    • (1977) Lgorithms for Chemical Computations
    • Tarjan, R.1
  • 49
    • 9344256091 scopus 로고    scopus 로고
    • Graph isomorphism completeness for chordal bipartite graphs and strongly chordal graphs
    • Uehara, R., Toda, S., and Nagoya, T. 2005. Graph isomorphism completeness for chordal bipartite graphs and strongly chordal graphs. Discrete Appl. Math. 145, 479-482.
    • (2005) Discrete Appl. Math. , vol.145 , pp. 479-482
    • Uehara, R.1    Toda, S.2    Nagoya, T.3
  • 50
    • 0001428106 scopus 로고    scopus 로고
    • Emcss: A new method for maximal common substructure search
    • Wang, T., and Zhou, J. 1997. EMCSS: a new method for maximal common substructure search. J. Chem. Inform. Comput. Sci. 37, 828-834.
    • (1997) J. Chem. Inform. Comput. Sci. , vol.37 , pp. 828-834
    • Wang, T.1    Zhou, J.2
  • 51
    • 0000656724 scopus 로고
    • Stereochemically unique naming algorithm
    • Wipke, W., and Dyott, T. 1974. Stereochemically unique naming algorithm. J. Am. Chem. Soc. 96, 4834-4842.
    • (1974) J. m. Chem. Soc. , vol.96 , pp. 4834-4842
    • Wipke, W.1    Dyott, T.2
  • 52
    • 0001970497 scopus 로고    scopus 로고
    • Gma: A generic match algorithm for structural homomorphism isomorhism and maximal common substructure match and its applications
    • Xu, J., 1996. GMA: A generic match algorithm for structural homomorphism, isomorhism, and maximal common substructure match and its applications. J. Chem. Inform. Comput. Sci. 36, 25-34.
    • (1996) J. Chem. Inform. Comput. Sci. , vol.36 , pp. 25-34
    • Xu, J.1
  • 53
    • 66349127228 scopus 로고    scopus 로고
    • E-zyme: Predicting potential ec numbers from the chemical transformation pattern of substrate-product pairs
    • Yamanishi, Y., Hattori, M., Kotera, M., et al. 2009. E-zyme: predicting potential ec numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics 25, 179-186.
    • (2009) Bioinformatics , vol.25 , pp. 179-186
    • Yamanishi, Y.1    Hattori, M.2    Kotera, M.3


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