In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism | Zendy

Masanori Arita | Zendy

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In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism

Author(s) -

Masanori Arita

Publication year - 2003

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.1212003

Subject(s) - tracing , in silico , substrate (aquarium) , biology , database , software , escherichia coli , product (mathematics) , computational biology , computer science , biological system , combinatorial chemistry , biochemistry , chemistry , programming language , mathematics , gene , ecology , geometry

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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