Computational Metabolism

This document provides an annotated bibliography on research in the area of computational metabolism. This interdisciplinary research field applies computational techniques to the study of biochemical pathways.

Surveys of Computational Metabolism

Galper, A. R. and Brutlag, D. L. (1994). Computational Simulations of Biological Systems. In Smith, D. W. (Ed.), Biocomputing: Informatics and Genome Projects (pp. 269-306.). New York NY: Academic Press.

P. Karp and M. Mavrovouniotis, "Representing, analyzing, and synthesizing biochemical pathways," IEEE Expert, 1994. in press.

Kazic, T., "Representation, Reasoning, and the Intermediary Metabolism of Escherichia coli", in Proc. of the 26th Annual Hawaii International Conference on System Sciences, 1993, I:853-862, IEEE Computer Society Press.

Metabolic Databases

Bairoch, A., "The ENZYME Databank in 1995", Nucleic Acids Research, 1996, 24:221-222.

Barcza, S. and Kelly, L.A. and Lenz, C.D., "Computerized Retrieval of Information on Biosynthesis and Metabolic Pathways," J. Chem. Inf. Comput. Sci., 1990, 30:243-251.

P.Karp, M. Riley, S. Paley, and A. Pellegrini-Toole, "EcoCyc: Electronic encyclopedia of E. coli genes and metabolism," Nuc. Acids Res., 24(1):32-40, 1996.

P.Karp, M. Riley, S. Paley, and A. Pellegrini-Toole, "EcoCyc: Electronic encyclopedia of E. coli genes and metabolism," Nuc. Acids Res., 25(1), 1997.

P. Karp and S. Paley, "Representations of metabolic knowledge: Pathways," in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (Altman, R. and Brutlag, D. and Karp, P. and Lathrop, R. and Searls, D. eds.), AAAI Press (Menlo Park, CA), 1994.

P. Karp and M. Riley, "Representations of metabolic knowledge," in Proceedings of the First International Conference on Intelligent Systems for Molecular biology (L. Hunter, D. Searls, and J. Shavlik, eds.), pp. 207-215, AAAI Press (Menlo Park, CA), 1993.

Kazic, T., "Biochemical databases: Challenges and opportunities", in Thirteenth International CODATA Conference, 1993.

Ochs, R.S. and Conrow, K., "A Computerized Metabolic Map", J. Chem. Inf. Comput. Sci., 1991, 31:132-137.

Reddy, V.N. and Mavrovouniotis, M.L. and Liebman, M.N., "Petri Net Representations in Metabolic Pathways", in Proceedings of the First International Conference on Intelligent Systems for Molecular Biology (L. Hunter, D. Searls, and J. Shavlik, eds.), (Menlo Park, CA), pp328-336.

Rouxel, T. and Danchin, A. and Henaut, A., "METALGEN.DB: Metabolism linked to the genome for Escherichia coli, graphics oriented database", Computer Applications in the Biosciences, 1993, 9(3):315-324.

Selkov, E. and Basmanova, S. and Gaasterland, T. and Goryanin, I. and Gretchkin, Y. and Maltsev, N. and Nenashev, V. and Overbeek, R. and Panyushkina, E. and Pronevitch, L. and Selkov, E. Jr and Yunus, I., "The metabolic pathway collection from EMP: The metabolic pathways database", in Nuc. Acids Res, 1996, 24(1):26-29.

Selkov, E. and Galimova, M. and Goryanin, I. and Gretchkin, Y. and Ivanova, N. and Komarov, Y. and Maltsev, N. and Mikhailova, N. and Nenashev, V. and Overbeek, R. and Panyushkina, E. and Pronevitch, L. and Selkov, E. Jr, "The metabolic pathway collection: an update", Nuc. Acids Res, 1997, 25(1):37-38.

Selkov, E.E. and Goryanin, I.I. and Kaimatchnov, N.P. and Shevelev, E.L. and Yunus, I.A., "Factographic data bank on enzymes and metabolic pathways", Studia Biophysica, 1989, 129(2-3):155-164.

Suyama, M. and Ogiwara, A. and Nishioka, T. and Oda, J., "Searching for amino acid sequence motifs among enzymes: the enzyme-reaction database," CABIOS, 9(1):9-15, 1993.

Pathway Analysis of Genomes

T. Gaasterland and E. Selkov, "Reconstruction of Metabolic Networks Using Incomplete Information," in Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, AAAI Press (Menlo Park, CA), pp127-135, 1995.

P. D. Karp, C. Ouzounis, and S. M. Paley, "HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae," in Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, AAAI Press (Menlo Park, CA), 1996.

Pathway Evolution

Baldwin, J. E., and H. Krebs (1981) "The evolution of metabolic cycles" Nature 291: 381-382.

Belfaiza, J., et al. (1986) "Evolution in biosynthetic pathways: two enzymes catalyzing consecutive steps in methionine biosynthesis originate from a common ancestor and possess a similar regulatory region" Proc. Natl. Acad. Sci. USA 83: 867-871.

Clarke, P. H. (1980) "Experiments in microbial evolution: new enzymes, new metabolic activities" Proc. R. Soc. Lond. B 207: 385-404.

Crawford, I. P. (1989) "Evolution of a biosynthetic pathway: the tryptophan paradigm" Ann. Rev. Microbiol. 43: 567-600.

Dickerson, R. E., R. Timkovich, and R. J. Almassy (1976) "The cytochrome fold and the evolution of bacterial energy metabolism" J. Mol. Biol. 100: 473-491.

Fothergill-Gilmore, L. A. (1986) "The evolution of the glycolytic pathway" Trends Biochem. Sci. 11: 47-51.

Fothergill-Gilmore, L. A., and P. A. M. Michels (1993) "Evolution of glycolysis" Progr. Biophys. Mol. Biol. 59: 105-235.

Hall, B. G. (1983) "Evolution of new metabolic functions in laboratory organisms" Evolution of genes and proteins, eds. M. Nei, and R. K. Koehn. (Sunderland, MA: Sinauer Associates Inc.) pp. 234-257.

Jukes, T. H., and J. L. King (1975) "Evolutionary loss of ascorbic acid synthesizing ability" J. Hum. Evol. 4: 85-88.

Lebioda, L., and B. Stec (1988) "Crystal structure of enolase indicates that enolase and pyruvate kinase evolved from a common ancestor" Nature 333: 683-686.

Meléndez-Hevia, E., and N. V. Torres (1988) "Economy of design in metabolic pathways: further remarks on the game of the pentose phosphate cycle" J. Theor. Biol. 132: 97-111.

Muirhead, H., and H. Watson (1992) "Glycolytic enzymes: from hexose to pyruvate" Curr. Opin. Struct. Biol. 2: 870-876.

Neidhart, D. J., et al. (1990) "Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous" Nature 347: 692-694.

Ouzounis, C., and C. Sander (1993) "Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes" FEBS Lett. 322: 159-164.

Woese, C. R. (1987) "Bacterial evolution" Microbiol. Rev. 51: 221-271.

Metabolic Simulation

Brutlag, D.G. and Galper, A.R. and Millis, D.H., "Knowledge-based Simulation of DNA metabolism: prediction of enzyme action", Computer Applications in the Biosciences, 1991, 7(1):9-19.

Brutlag, D. L. (1988). Expert System Simulations as Active Learning Environments. In Colwell, R. R. (Ed.), Biomolecular Data: A Resource in Transition (pp. 185-188.). Oxford: Oxford University Press.

Cohen, D.M. and Bergman, R.N., "Prediction of positional isotopomers of the citric acid cycle: the syntactic approach", Am J Physiology, 1994, 266(3):341-50.

Cohen, D.M. and Bergman, R.N., "SYNTAX: A rule-based stochastic simulation of the time-varying concentrations of positional isotopomers of metabolic intermediates", Computers and Biomedical Research, 1994, 27:130-147.

Galper, A. R., Millis, D. H. and Brutlag, D. L. (1993). Knowledge-Based Simulation of DNA metabolism: Prediction of Action and Envisionment of Pathways, In Hunter, L. (Ed.), Artificial Intelligence in Molecular Biology (pp. 365-395). AAAI Press (Menlo Park, CA).

Mavrovouniotis, M. L. and Stephanopoulos, G. and Stephanopoulos, G., "Formal Modelling of Approximate Relations in Biochemical Systems", Biotechnology and Bioengineering, 1989, 34(2):196-206.

Selkov has shown (Eur. J. Biochem., 1975, 59(1), 151-157) that the stoichiometric structure of glycolytic and other types of energy supplying systems can perfectly stabilize Atkinson's adenylate energy charge. The experimental proof of this theoretical prediction has been made much later by Arnold Boiteux in a collaboration with Selkov in Dortmund (A. Boiteux, B. Hess, and E. E. Selkov, In: Eur. J. BiochemSelf-organization. Autowaves and structures far from equilibrium. (V. I. Krinsky, ed.), Springer-Verlag, Berlin, 1984, p. 240-251.)

Design of Metabolic Pathways for Biotechnology

Bailey, J.E., "Toward a Science of Metabolic Engineering", Science, 1991, 252:1668-1675, June.

Cameron, C. and Tong, I., "Cellular and Metabolic Engineering: An Overview", Applied Biochemistry and Biotechnology, 1993, 38:105-140.

Seressiotis, A. and Bailey, J.E., "MPS: An Artificially Intelligent Software System for the Analysis and Synthesis of Metabolic Pathways", Biotechnology and Bioengineering, 1988, 31:587-602.

Stephanopoulos, G. and Vallino, J.J., "Network rigidity and metabolic engineering in metabolite overproduction", Science, 1991, 252:1675-1681, June.

Search for Routes in Metabolic Networks

Mavrovouniotis, M. L., "Identification of Qualitatively Feasible Metabolic Pathways", in Artificial Intelligence and Molecular Biology, AAAI Press / MIT Press, 1993, L. Hunter.

Mavrovouniotis, M.L., "Computer-Aided Design of Biochemical Pathways", PhD dissertation from Massachusetts Institute of Technology, 1989.

Metabolites

P. D. Karp, "A knowledge base of the chemical compounds of intermediary metabolism," CABIOS, vol. 8, no. 4, pp. 347-357, 1992.

Kazic, T., "Reasoning about biochemical compounds and processes", in Proceedings of the Second International Conference on Bioinformatics, Supercomputing and the Human Genome Project, pp35-49.

Mavrovouniotis, M. L., "Estimation of Standard Gibbs Energy Changes of Biotransformations", Journal of Biological Chemistry, 1991, 266(22):14440-14445.

Mavrovouniotis, M., "Group Contributions for Estimating Standard Gibbs Energies of Formation of Biochemical Compounds in Aqueous Solution", Biotechnology and Bioengineering, 1990, 36:1070-1082.

Automatic Drawing of Metabolic Pathways

P. Karp and S. M. Paley, Automated drawing of metabolic pathways," in Third International Conference on Bioinformatics and Genome Research (H. Lim, C. Cantor, and R. Robbins, eds.), 1994.

P. Karp and S. Paley, "Integrated access to metabolic and genomic data," Journal of Computational Biology 3:191-212 1996.

Maintained by Peter D. Karp