title: In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism.
abstract: We present a software system that computationally reproduces biochemical radioisotope-tracer experiments. It consists of three main components: A mapping database of substrate-product atomic correspondents derived from known reaction formulas, a tracing engine that can compute all pathways between two given compounds by using the mapping database, and a graphical user interface. As the system can facilitate the display of all possible pathways between any two compounds and the tracing of every single carbon, nitrogen, or sulfur atom in the metabolism, it complements and bridges other metabolic databases and simulations on fixed models.
authors.affiliation: Department of Computational Biology, Faculty of Frontier Sciences, The University of Tokyo and PRESTO, JST, 277-8561 Kashiwa, Japan. arita@k.u-tokyo.ac.jp
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
mesh_terms: D002244:Carbon / Q000378:metabolism; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D003198:Computer Simulation / Q000706:statistics & numerical data; D016208:Databases, Factual; D004926:Escherichia coli / Q000201:enzymology / Q000378:metabolism*; D009584:Nitrogen / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods / Q000706:statistics & numerical data; D012984:Software; D013379:Substrate Specificity; D013455:Sulfur / Q000378:metabolism; D014153:Transaldolase / Q000737:chemistry / Q000378:metabolism; D000637:Transaminases / Q000737:chemistry / Q000378:metabolism
chemical_list: D013455:Sulfur; D002244:Carbon; D014153:Transaldolase; D000637:Transaminases; C022638:serine-pyruvate aminotransferase; D009584:Nitrogen