The idea of Enzyme-Centric modeling is to understand common enzyme catalytic and regulatory mechanisms in biological processes then integrate individual enzyme models into a pathway and finally assemble the various pathways into a larger biological system. This approach incorporates non-linear properties of biological pathways, such as positive/negative feedback and allosteric regulation, reversible enzyme reactions, biological redundancy (isoforms), multifunctional enzymes and multifunctional pathways. In contrast, the commonly linear molecular conversion modeling assumes enzymes are constant and ignores the enzyme regulatory mechanisms to simplify the complexity of the biological models. Thus, only the non-linear model incorporating the continually changing status/partition of enzymes in a biological system can allow pathway-specific patterns to be identified.

We have developed kMech (kinetic mechanism), a comprehensive collection of single and multiple substrate enzyme reactions and regulatory mechanisms, that extends the funtionality of Cellerator for modeling complex enzyme reactions. Each mechanism has been codified to generate a set of elementary reactions that can be translated by Cellerator into ordinary differential equations (ODEs) solvable by MathematicaTM . We have also developed methods that use common kinetic measurements to estimate physical constants required to solve these ODEs. Because kMech assembles fundamental modular association-dissociation reaction mechanisms to describe complex enzyme mechanisms, the kMech/Cellerator dynamic modeling system is more flexible and easily extended than commonly used Michaelis-Menten kinetic equations.