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Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(6):774-780; doi:10.1093/bioinformatics/bti068
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

An enzyme mechanism language for the mathematical modeling of metabolic pathways

Chin-Rang Yang 1,3, Bruce E. Shapiro 4, Eric D. Mjolsness 2,3 and G. Wesley Hatfield 1,3,*

1Department of Microbiology and Molecular Genetics, College of Medicine, University of California Irvine, CA 92697, USA
2School of Information and Computer Science, University of California Irvine, CA 92697, USA
3Institute for Genomics and Bioinformatics, University of California Irvine, CA 92697, USA
4Jet Propulsion Laboratory, California Institute of Technology 4800 Oak Grove Drive, Pasadena, CA 91109, USA

*To whom correspondence should be addressed.

Motivation: As a first step toward the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways.

Results: We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association–dissociation reactions that are translated by Cellerator into ordinary differential equations that are numerically solved by MathematicaTM. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.

Availability: A MathematicaTM executable kMech.m file is available at the University of California, Irvine, Institute for Genomics and Bioinformatics website, http://www.igb.uci.edu/servers/sb.html. Cellerator, free of charge to academic, US government, and other non-profit organizations, can be obtained at the Cellerator website, (http://www-aig.jpl.nasa.gov/public/mls/cellerator/feedback.html).

Contact: Biology correspondence should be addressed to gwhatfie{at}uci.edu. Computation correspondence should be addressed to emj{at}uci.edu.

Supplementary information: http://www.igb.uci.edu/servers/sb.html.


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