Bibliography of: Glycolysis

  1. Hofestadt, R. and Thelen, S.. "Quantitative modeling of biochemical networks." In Silico Biol. 1 (1). 1998. pp. 39-53.
    [ PubMed ] [ WebSite ]

    Today different database systems for molecular structures (genes and proteins) and metabolic pathways are available. All these systems are characterized by the static data representation. For progress in biotechnology the dynamic representation of this data is important. The metabolism can be characterized as a complex biochemical network. Different models for the quantitative simulation of biochemical networks are discussed, but no useful formalization is available. This paper shows that the theory of Petrinets is useful for the quantitative modeling of biochemical networks.

    Keywords: *Biochemistry ; Biotechnology ; Catalysis ; Computational Biology ; *Computer Simulation ; Databases Factual ; Glycolysis ; Models Biological ; Protein Engineering


  2. Kuffner, R., Zimmer, R., and Lengauer, T.. "Pathway analysis in metabolic databases via differential metabolic display (DMD)." Bioinformatics. 16 (9). 2000. pp. 825-36.
    [ .pdf ] [ PubMed ] [ WebSite ]

    MOTIVATION: A number of metabolic databases are available electronically, some with features for querying and visualizing metabolic pathways and regulatory networks. We present a unifying, systematic approach based on PETRI nets for storing, displaying, comparing, searching and simulating such nets from a number of different sources. RESULTS: Information from each data source is extracted and compiled into a PETRI net. Such PETRI nets then allow to investigate the (differential) content in metabolic databases, to map and integrate genomic information and functional annotations, to compare sequence and metabolic databases with respect to their functional annotations, and to define, generate and search paths and pathways in nets. We present an algorithm to systematically generate all pathways satisfying additional constraints in such PETRI nets. Finally, based on the set of valid pathways, so-called differential metabolic displays (DMDs) are introduced to exhibit specific differences between biological systems, i.e. different developmental states, disease states, or different organisms, on the level of paths and pathways. DMDs will be useful for target finding and function prediction, especially in the context of the interpretation of expression data.

    Keywords: *Algorithms ; Catalysis ; Computational Biology_*methods ; Computer Simulation ; *Data Display ; *Databases Factual ; Enzymes_genetics ; Enzymes_metabolism ; Glycolysis ; Metabolism_*physiology ; Mycoplasma_metabolism ; Yeasts_metabolism


  3. Mavrovouniotis, M.L.. "Identification of localized and distributed bottlenecks in metabolic pathways." Proc Int Conf Intell Syst Mol Biol. vol. 1. 1993. pp. 275-83.
    [ PubMed ]

    The usual thermodynamic evaluation, based solely on the Standard Gibbs Energy of reaction, does not take into account the permissible ranges of concentrations of metabolites, and it faces further difficulties when, instead of isolated reactions, we are examining whole pathways. For pathways, we seek not only to decide whether they are feasible but also to pinpoint the pathway segment that causes any thermodynamic difficulties. We define a set of scaled quantities which reformulate the thermodynamic-feasibility problem for the whole pathway. We present an algorithm which analyzes individual reactions and selective construction of larger subpathways and uncovers localized and distributed thermodynamic bottlenecks of the biotransformation. This type of thermodynamic treatment contributes to the effort to include more physical, chemical, and biological factors in the computer-aided analysis of metabolic pathways.

    Keywords: *Algorithms ; *Computer Simulation ; Glycolysis ; *Metabolism ; *Models Biological ; *Thermodynamics