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 Mathematica. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.
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 Mathematica. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.
Authors: Behnam Compani; Trent Su; Ivan Chang; Jianlin Cheng; Kandarp H Shah; Thomas Whisenant; Yimeng Dou; Adriel Bergmann; Raymond Cheong; Barbara Wold; Lee Bardwell; Andre Levchenko; Pierre Baldi; Eric Mjolsness Journal: Adv Exp Med Biol Date: 2010 Impact factor: 2.622
Authors: Andreas Dräger; Marcel Kronfeld; Michael J Ziller; Jochen Supper; Hannes Planatscher; Jørgen B Magnus; Marco Oldiges; Oliver Kohlbacher; Andreas Zell Journal: BMC Syst Biol Date: 2009-01-14