DATABASE: Biochemistry One Step at a Time

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Science  30 Jan 2004:
Vol. 303, Issue 5658, pp. 601
DOI: 10.1126/science.303.5658.601b

Building a molecule of heme, the oxygen-hauling core of hemoglobin, isn't simple: Starting from the amino acid L-glycine, it takes eight steps and requires a coenzyme, oxygen, water, and iron. Researchers can scrutinize the details of this and hundreds of other biochemical conversions at BioCyc, sponsored by the nonprofit institute SRI International of Menlo Park, California.

The site furnishes databases of metabolic pathways for humans and 13 microbes, including the stomach-churning O157:H7 strain of Escherichia coli and two variants of Mycobacterium tuberculosis, causes of the lung disease. By clicking on diagrams for a particular set of chemical transformations, users can glean information such as the molecular weight and structure of the products and reactants as well as the protein and DNA sequences of the enzymes involved. A program that parses the organism's genome and predicts likely linkages derived most of the pathways. But the site also features MetaCyc, a collection of biochemical information for 150 creatures drawn from the literature. Users can search the databases online, but SRI also offers downloadable versions and analysis tools that are free upon request for academic researchers.

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