title: An enzyme mechanism language for the mathematical modeling of metabolic pathways.
abstract: 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.
authors.affiliation: Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA.
authors.forename: Chin-Rang
authors.initials: CR
authors.lastname: Yang
authors.forename: Bruce E
authors.initials: BE
authors.lastname: Shapiro
authors.forename: Eric D
authors.initials: ED
authors.lastname: Mjolsness
authors.forename: G Wesley
authors.initials: GW
authors.lastname: Hatfield
mesh_terms: 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*
chemical_list: D004798:Enzymes