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.
Footnotes
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1212003. Article published online before print in October 2003.
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[The software and data files for the Escherichia coli metabolism (MOL-format files for molecular structures, reaction formulas for enzymes, and mapping information at the atomic level) are available at http://www.metabolome.jp/.]
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- Accepted July 23, 2003.
- Received January 23, 2003.
- Cold Spring Harbor Laboratory Press
