메뉴 건너뛰기




Volumn 59, Issue 22-23, 2004, Pages 5051-5060

Computational discovery of biochemical routes to specialty chemicals

Author keywords

7 Carboxyindole; Automated network generation; Graph theory; Group additivity; Novel biochemical pathways

Indexed keywords

ALGORITHMS; CATALYST ACTIVITY; CHEMICAL ACTIVATION; COMPUTABILITY AND DECIDABILITY; ENZYMES; EVALUATION; FUNCTIONS; GRAPH THEORY; SUBSTRATES;

EID: 8744251043     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ces.2004.09.021     Document Type: Conference Paper
Times cited : (71)

References (58)
  • 2
    • 0028410110 scopus 로고
    • Computer generated pyrolysis modelling: On-the-fly generation of reactions, rates and predictions
    • Broadbelt, L.J., Stark, S.M., Klein, M.T., 1994. Computer generated pyrolysis modelling: on-the-fly generation of reactions, rates and predictions. Industrial and Engineering Chemistry Research 33 (4), 790-799.
    • (1994) Industrial and Engineering Chemistry Research , vol.33 , Issue.4 , pp. 790-799
    • Broadbelt, L.J.1    Stark, S.M.2    Klein, M.T.3
  • 3
    • 0000670212 scopus 로고
    • Termination of computer-generated reaction mechanisms: Species rank-based convergence criterion
    • Broadbelt, L.J., Stark, S.M., Klein, M.T., 1995. Termination of computer-generated reaction mechanisms: species rank-based convergence criterion. Industrial and Engineering Chemistry Research 34, 2566-2573.
    • (1995) Industrial and Engineering Chemistry Research , vol.34 , pp. 2566-2573
    • Broadbelt, L.J.1    Stark, S.M.2    Klein, M.T.3
  • 4
    • 0030086839 scopus 로고    scopus 로고
    • Computer generated reaction modelling: Decomposition and encoding algorithms for determining species uniqueness
    • Broadbelt, L.J., Stark, S.M., Klein, M.T., 1996. Computer generated reaction modelling: decomposition and encoding algorithms for determining species uniqueness. Computer & Chemical Engineering 20 (2), 113-129.
    • (1996) Computer & Chemical Engineering , vol.20 , Issue.2 , pp. 113-129
    • Broadbelt, L.J.1    Stark, S.M.2    Klein, M.T.3
  • 5
    • 0000948052 scopus 로고
    • Detoxication of drugs and other foreign compounds by liver microsomes
    • Brodie, B.B., et al., 1955. Detoxication of drugs and other foreign compounds by liver microsomes. Science (Washington, DC, United States) 121, 603-604.
    • (1955) Science (Washington, DC, United States) , vol.121 , pp. 603-604
    • Brodie, B.B.1
  • 7
    • 0021215984 scopus 로고
    • Computer-generation of reaction paths and rate equations in the thermal cracking of normal and branched paraffins
    • Clymans, P.J., Froment, G.F., 1984. Computer-generation of reaction paths and rate equations in the thermal cracking of normal and branched paraffins. Computers and Chemical Engineering 8, 137-142.
    • (1984) Computers and Chemical Engineering , vol.8 , pp. 137-142
    • Clymans, P.J.1    Froment, G.F.2
  • 8
    • 0035281870 scopus 로고    scopus 로고
    • Metabolic modeling of microbial strains in silico
    • Covert, M.W., et al., 2001. Metabolic modeling of microbial strains in silico. Trends in Biochemical Sciences 26 (3), 179-186.
    • (2001) Trends in Biochemical Sciences , vol.26 , Issue.3 , pp. 179-186
    • Covert, M.W.1
  • 9
    • 12444313031 scopus 로고    scopus 로고
    • Indole amide hydroxamic acids as potent inhibitors of histone deacetylases
    • Dai, Y., et al., 2003. Indole amide hydroxamic acids as potent inhibitors of histone deacetylases. Bioorganic & Medicinal Chemistry Letters 13 (11), 1897-1901.
    • (2003) Bioorganic & Medicinal Chemistry Letters , vol.13 , Issue.11 , pp. 1897-1901
    • Dai, Y.1
  • 10
    • 0034234864 scopus 로고    scopus 로고
    • Computer generation of reaction mechanisms using quantitative rate information: Application to long-chain hydrocarbon pyrolysis
    • De Witt, M.J., Dooling, D.J., Broadbelt, L.J., 2000. Computer generation of reaction mechanisms using quantitative rate information: application to long-chain hydrocarbon pyrolysis. Industrial and Engineering Chemistry Research 39 (7), 2228-2237.
    • (2000) Industrial and Engineering Chemistry Research , vol.39 , Issue.7 , pp. 2228-2237
    • De Witt, M.J.1    Dooling, D.J.2    Broadbelt, L.J.3
  • 12
    • 0002754254 scopus 로고
    • The generation of reaction networks with rain. 1. The reaction generator
    • Fontain, E., Reitsam, K., 1991. The generation of reaction networks with rain. 1. The reaction generator. J. Chem. Inf. Comput. Sci. 31, 96-101.
    • (1991) J. Chem. Inf. Comput. Sci. , vol.31 , pp. 96-101
    • Fontain, E.1    Reitsam, K.2
  • 13
    • 21144466098 scopus 로고
    • Thermodynamics of enzyme-catalyzed reaction: Part 1. Oxidoreductases
    • Goldberg, R.N., et al., 1993. Thermodynamics of enzyme-catalyzed reaction: Part 1. Oxidoreductases. Journal of Physical and Chemical Reference Data 22 (515),
    • (1993) Journal of Physical and Chemical Reference Data , vol.22 , Issue.515
    • Goldberg, R.N.1
  • 14
    • 10044249400 scopus 로고    scopus 로고
    • Preparation of (s)-α-methyltryptophan amide derivatives as bombesin receptor antagonists
    • Wo: Warner-Lambert Company, USA
    • Higginbottom, M., Pritchard, M.C., Stock, H.T., 2002. Preparation of (s)-α-methyltryptophan amide derivatives as bombesin receptor antagonists. PCT International Applications 85pp. Wo: Warner-Lambert Company, USA.
    • (2002) PCT International Applications
    • Higginbottom, M.1    Pritchard, M.C.2    Stock, H.T.3
  • 15
    • 0023842254 scopus 로고
    • Computer generation of reaction schemes and rate equations for thermal cracking
    • Hillewaert, L.P., Dierickx, J.L., Froment, G.F., 1988. Computer generation of reaction schemes and rate equations for thermal cracking. A.I.Ch.E Journal 34, 17-24.
    • (1988) A.I.Ch.E Journal , vol.34 , pp. 17-24
    • Hillewaert, L.P.1    Dierickx, J.L.2    Froment, G.F.3
  • 16
    • 0004857317 scopus 로고
    • Synthesis in the indole series. 3. Preparation of 5-, 6-, and 7-cyano and -carboxyindolines and -indoles
    • Ikan, R., Rapaport, E., 1967. Synthesis in the indole series. 3. Preparation of 5-, 6-, and 7-cyano and -carboxyindolines and -indoles. Tetrahedron 23 (9), 3823-3827.
    • (1967) Tetrahedron , vol.23 , Issue.9 , pp. 3823-3827
    • Ikan, R.1    Rapaport, E.2
  • 17
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M.G.S., 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28, 27-30.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.G.S.1
  • 18
    • 0035860545 scopus 로고    scopus 로고
    • Pathway databases: A case study in computational symbolic theories
    • Karp, P.D., 2001. Pathway databases: a case study in computational symbolic theories. Science (Washington, DC, United States) 293 (5537), 2040-2044.
    • (2001) Science (Washington, DC, United States) , vol.293 , Issue.5537 , pp. 2040-2044
    • Karp, P.D.1
  • 19
    • 10044271461 scopus 로고
    • Bis(3-indolyl)phthalides and their spectral properties
    • Karymova, T.M., et al., 1989. Bis(3-indolyl)phthalides and their spectral properties. Khimiya Geterotsiklicheskikh Soedinenii (7), 915-918.
    • (1989) Khimiya Geterotsiklicheskikh Soedinenii , Issue.7 , pp. 915-918
    • Karymova, T.M.1
  • 22
    • 0033423672 scopus 로고    scopus 로고
    • META. Part 4. Prediction of the metabolism of polycyclic aromatic hydrocarbons
    • Klopman, G., Tu, M., Fan, B.T., 1999. META. Part 4. Prediction of the metabolism of polycyclic aromatic hydrocarbons. Theoretical Chemistry Accounts 102 (1-6), 33-38.
    • (1999) Theoretical Chemistry Accounts , vol.102 , Issue.1-6 , pp. 33-38
    • Klopman, G.1    Tu, M.2    Fan, B.T.3
  • 23
    • 10044297806 scopus 로고    scopus 로고
    • Method for producing trimer of indole derivative by oxidative cyclotrimerization of indole derivative, and trimer of indole derivative and laminated structure thereof
    • Wo: Mitsubishi Rayon Co., Ltd., Japan
    • Maeda, S., et al., 2002. Method for producing trimer of indole derivative by oxidative cyclotrimerization of indole derivative, and trimer of indole derivative and laminated structure thereof, PCT International Applications: 107pp. Wo: Mitsubishi Rayon Co., Ltd., Japan.
    • (2002) PCT International Applications
    • Maeda, S.1
  • 24
    • 0004779396 scopus 로고
    • Mechanisms of oxygen metabolism
    • Mason, H.S., 1957. Mechanisms of oxygen metabolism. Science 125, 1185-1188.
    • (1957) Science , vol.125 , pp. 1185-1188
    • Mason, H.S.1
  • 25
    • 0242286046 scopus 로고    scopus 로고
    • Mechanism generation with integrated pressure dependence: A new model for methane pyrolysis
    • Matheu, D.M., et al., 2003a. Mechanism generation with integrated pressure dependence: a new model for methane pyrolysis. Journal of Physical Chemistry A 107 (41), 8552-8565.
    • (2003) Journal of Physical Chemistry A , vol.107 , Issue.41 , pp. 8552-8565
    • Matheu, D.M.1
  • 26
    • 0037373709 scopus 로고    scopus 로고
    • Capturing pressure-dependence in automated mechanism generation: Reactions through cycloalkyl intermediates
    • Matheu, D.M., Green, W.H., Grenda, J.M., 2003b. Capturing pressure-dependence in automated mechanism generation: reactions through cycloalkyl intermediates. International Journal of Chemical Kinetics 35 (3), 95-119.
    • (2003) International Journal of Chemical Kinetics , vol.35 , Issue.3 , pp. 95-119
    • Matheu, D.M.1    Green, W.H.2    Grenda, J.M.3
  • 28
    • 0025701406 scopus 로고
    • Group contributions for estimating standard gibbs energies of formation of biochemical-compounds in aqueous-solution
    • Mavrovouniotis, M.L., 1990. Group contributions for estimating standard gibbs energies of formation of biochemical-compounds in aqueous-solution. Biotechnology and Bioengineering 36 (10), 1070-1082.
    • (1990) Biotechnology and Bioengineering , vol.36 , Issue.10 , pp. 1070-1082
    • Mavrovouniotis, M.L.1
  • 29
    • 0026353854 scopus 로고
    • Estimation of standard Gibbs energy changes of biotransformations
    • Mavrovouniotis, M.L., 1991. Estimation of standard Gibbs energy changes of biotransformations. Journal of Biological Chemistry 266 (22), 14440-14445.
    • (1991) Journal of Biological Chemistry , vol.266 , Issue.22 , pp. 14440-14445
    • Mavrovouniotis, M.L.1
  • 32
    • 0003450992 scopus 로고
    • Academic Press, New York
    • (NC-IUBMB), Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. (1992). Enzyme Nomenclature. Academic Press, New York.
    • (1992) Enzyme Nomenclature
  • 34
    • 10044267113 scopus 로고
    • U.S.S.R. Su: Institute of Physical-Organic Chemistry and Coal Chemistry, Academy of Sciences, Ukrainian S.S.R., USSR
    • Nikolyukin, Y.A., et al. 1984. Indole-7-carboxylic acid. U.S.S.R. Su: Institute of Physical-Organic Chemistry and Coal Chemistry, Academy of Sciences, Ukrainian S.S.R., USSR.
    • (1984) Indole-7-carboxylic Acid
    • Nikolyukin, Y.A.1
  • 35
    • 0030461967 scopus 로고    scopus 로고
    • Synthesis and evaluation of heterocyclic carboxamides as potential antipsychotic agents
    • Norman, M.H., et al., 1996. Synthesis and evaluation of heterocyclic carboxamides as potential antipsychotic agents. Journal of Medicinal Chemistry 39 (24), 4692-4703.
    • (1996) Journal of Medicinal Chemistry , vol.39 , Issue.24 , pp. 4692-4703
    • Norman, M.H.1
  • 36
    • 0031554858 scopus 로고    scopus 로고
    • Construction of complex reaction systems. 1. Reaction description language
    • Prickelt, S.E., Mavrovouniotis, M.L., 1997a. Construction of complex reaction systems. 1. Reaction description language. Computers & Chemical Engineering 21, 1219-1235.
    • (1997) Computers & Chemical Engineering , vol.21 , pp. 1219-1235
    • Prickelt, S.E.1    Mavrovouniotis, M.L.2
  • 37
    • 0031554860 scopus 로고    scopus 로고
    • Construction of complex reaction systems. 2. Molecule manipulation and reaction application algorithms
    • Prickelt, S.E., Mavrovouniotis, M.L., 1997b. Construction of complex reaction systems. 2. Molecule manipulation and reaction application algorithms. Computers & Chemical Engineering 21, 1237-1254.
    • (1997) Computers & Chemical Engineering , vol.21 , pp. 1237-1254
    • Prickelt, S.E.1    Mavrovouniotis, M.L.2
  • 38
    • 0031220244 scopus 로고    scopus 로고
    • Construction of complex reaction systems. 3. An example: Alkylation of olefins
    • Prickett, S.E., Mavrovouniotis, M.L., 1997c. Construction of complex reaction systems. 3. An example: alkylation of olefins. Computers & Chemical Engineering 21, 1325-1337.
    • (1997) Computers & Chemical Engineering , vol.21 , pp. 1325-1337
    • Prickett, S.E.1    Mavrovouniotis, M.L.2
  • 40
    • 0028273009 scopus 로고
    • Discovery, synthesis, and bioactivity of bis(heteroaryl)piperazines. 1. A novel class of non-nucleoside HIV-1 reverse transcriptase inhibitors
    • Romero, D.L., et al., 1994. Discovery, synthesis, and bioactivity of bis(heteroaryl)piperazines. 1. A novel class of non-nucleoside HIV-1 reverse transcriptase inhibitors. Journal of Medicinal Chemistry 37 (7), 999-1014.
    • (1994) Journal of Medicinal Chemistry , vol.37 , Issue.7 , pp. 999-1014
    • Romero, D.L.1
  • 41
    • 0026603416 scopus 로고
    • Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism
    • Savinell, J.M., Palsson, B.O., 1992. Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism. Journal of Theoretical Biology 154 (4), 455-473.
    • (1992) Journal of Theoretical Biology , vol.154 , Issue.4 , pp. 455-473
    • Savinell, J.M.1    Palsson, B.O.2
  • 42
    • 0034784809 scopus 로고    scopus 로고
    • META V. A model of photodegradation for the prediction of photoproducts of chemicals under natural-like conditions
    • Sedykh, A., Saiakhov, R., Klopman, G., 2001. META V. A model of photodegradation for the prediction of photoproducts of chemicals under natural-like conditions. Chemosphere 45 (6-7), 971-981.
    • (2001) Chemosphere , vol.45 , Issue.6-7 , pp. 971-981
    • Sedykh, A.1    Saiakhov, R.2    Klopman, G.3
  • 43
    • 0022971582 scopus 로고
    • MPS: An algorithm and data base for metabolic pathway synthesis
    • Seressiotis, A., Bailey, J.E., 1986. MPS: an algorithm and data base for metabolic pathway synthesis. Biotechnology Letters 8 (12), 837-842.
    • (1986) Biotechnology Letters , vol.8 , Issue.12 , pp. 837-842
    • Seressiotis, A.1    Bailey, J.E.2
  • 44
    • 0023995387 scopus 로고
    • MPS: An artificially intelligent software system for the analysis and synthesis of metabolic pathways
    • Seressiotis, A., Bailey, J.E., 1988. MPS: an artificially intelligent software system for the analysis and synthesis of metabolic pathways. Biotechnology and Bioengineering 31 (6), 587-602.
    • (1988) Biotechnology and Bioengineering , vol.31 , Issue.6 , pp. 587-602
    • Seressiotis, A.1    Bailey, J.E.2
  • 46
    • 10044284809 scopus 로고
    • Preparation of indole-7-carboxamide derivatives as analgesics. European Patent Applications Ep: Hoechst-Roussel Pharmaceutical Inc., USA
    • Shutske, G., 1994. Preparation of indole-7-carboxamide derivatives as analgesics. European Patent Applications: 16pp. Ep: Hoechst-Roussel Pharmaceutical Inc., USA.
    • (1994)
    • Shutske, G.1
  • 48
    • 0035933899 scopus 로고    scopus 로고
    • Emergence of multifunctional oxygenase activities by random priming recombination
    • Suenaga, H., et al., 2001. Emergence of multifunctional oxygenase activities by random priming recombination. Journal of Biological Chemistry 276, 22500-22506.
    • (2001) Journal of Biological Chemistry , vol.276 , pp. 22500-22506
    • Suenaga, H.1
  • 49
    • 0000064165 scopus 로고    scopus 로고
    • Rate-based construction of kinetic models for complex systems
    • Susnow, R.G., et al., 1997. Rate-based construction of kinetic models for complex systems. Journal of Physical Chemistry A 101, 3731-3740.
    • (1997) Journal of Physical Chemistry A , vol.101 , pp. 3731-3740
    • Susnow, R.G.1
  • 50
    • 0028534522 scopus 로고
    • META 2. A dictionary model of mammalian xenobiotic metabolism
    • Talafous, J., et al., 1994. META 2. A dictionary model of mammalian xenobiotic metabolism. Journal of Chemical Information and Computer Science 34 (6), 1326-1333.
    • (1994) Journal of Chemical Information and Computer Science , vol.34 , Issue.6 , pp. 1326-1333
    • Talafous, J.1
  • 52
    • 84986468452 scopus 로고
    • Algorithm to generate reaction pathways for computer-assisted elucidation
    • Valdes-Perez, R.E., 1992a. Algorithm to generate reaction pathways for computer-assisted elucidation. Journal of Comparative Chemistry 13, 1079-1088.
    • (1992) Journal of Comparative Chemistry , vol.13 , pp. 1079-1088
    • Valdes-Perez, R.E.1
  • 53
    • 5444261268 scopus 로고
    • A necessary condition for catalysis in reaction pathways
    • Valdes-Perez, R.E., 1992b. A necessary condition for catalysis in reaction pathways. Journal of Physical Chemistry 96, 2394-2396.
    • (1992) Journal of Physical Chemistry , vol.96 , pp. 2394-2396
    • Valdes-Perez, R.E.1
  • 54
    • 0002255427 scopus 로고
    • Human/computer interactive elucidation of reaction mechanisms: Application to catalyzed hydrogenolysis of ethane
    • Valdes-Perez, R.E., 1994. Human/computer interactive elucidation of reaction mechanisms: application to catalyzed hydrogenolysis of ethane. Catalysis Letters 28, 79-87.
    • (1994) Catalysis Letters , vol.28 , pp. 79-87
    • Valdes-Perez, R.E.1
  • 55
    • 0141651236 scopus 로고    scopus 로고
    • Interactive elucidation without programming of reaction mechanisms in heterogeneous catalysis
    • Valdes-Perez, R.E., Zeigarnik, A.V., 1997. Interactive elucidation without programming of reaction mechanisms in heterogeneous catalysis. Journal of Molecular Catalysis A: Chemical 119, 405-414.
    • (1997) Journal of Molecular Catalysis A: Chemical , vol.119 , pp. 405-414
    • Valdes-Perez, R.E.1    Zeigarnik, A.V.2
  • 56
    • 0027723421 scopus 로고
    • Metabolic capabilities of Escherichta colt. Ii. Optimal growth patterns
    • Varma, A., Palsson, B.O., 1993a. Metabolic capabilities of Escherichta colt. Ii. Optimal growth patterns. Journal of Theoretical Biology 165 (4), 503-522.
    • (1993) Journal of Theoretical Biology , vol.165 , Issue.4 , pp. 503-522
    • Varma, A.1    Palsson, B.O.2
  • 57
    • 0027716622 scopus 로고
    • Metabolic capabilities of Escherichia coli: I. Synthesis of biosynthetic precursors and cofactors
    • Varma, A., Palsson, B.O., 1993b. Metabolic capabilities of Escherichia coli: I. Synthesis of biosynthetic precursors and cofactors. Journal of Theoretical Biology 165 (4), 477-502.
    • (1993) Journal of Theoretical Biology , vol.165 , Issue.4 , pp. 477-502
    • Varma, A.1    Palsson, B.O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.