An enzyme mechanism language for the mathematical modeling of metabolic pathways.
BACKGROUND
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 Mathematica. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.
Yang
Chin-Rang
CR
Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA.
Shapiro
Bruce E
BE
Mjolsness
Eric D
ED
Hatfield
G Wesley
GW
D000465:Algorithms; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D005786:Gene Expression Regulation / Q000502:physiology; D008954:Models, Biological; D008956:Models, Chemical; D011381:Programming Languages; D015398:Signal Transduction / Q000502:physiology*
D004798:Enzymes