kMech

kMech parses and translates enzyme mechanisms into ordinary differential equation models for mathematical analysis of catalytic and regulatory reactions in signal transduction and metabolic pathways.

Key Features:

• Extension of Cellerator Language: Extends the Cellerator language with a suite of specialized enzyme mechanisms for modeling catalytic and regulatory processes.
• Parsing Enzyme Mechanisms: Parses each enzyme mechanism into fundamental association-dissociation reactions.
• Translation to Ordinary Differential Equations (ODEs): Translates the parsed association-dissociation reactions into ordinary differential equations (ODEs) for dynamic modeling.
• Numerical Solution with Mathematica: Solves the resulting ODE systems numerically using Mathematica.
• Estimation of Rate Constants: Estimates rate constants required for ODEs from commonly available kinetic measurements.

Scientific Applications:

• Systems Biology: Provides a mathematical framework for modeling enzyme-mediated regulation and interaction at the systems level.
• Signal Transduction Pathways: Models enzyme regulation and catalytic mechanisms within signal transduction pathways.
• Metabolic Pathway Analysis: Supports analysis of metabolic pathways by representing enzymatic reaction mechanisms and kinetics.

Methodology:

Parses enzyme mechanisms into association-dissociation reactions, translates them into ordinary differential equations (ODEs), estimates rate constants from common kinetic measurements, and numerically solves the ODEs in Mathematica.