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Genome Res. 2003 Nov;13(11):2455-66. Epub 2003 Oct 14.

In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism.

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  • 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


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.

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