Modeling Biochemical Pathways

Sequence analysis methods predict macromolecule properties and intermolecular interactions. These data can be used to reconstruct molecular networks, which are complex systems that regulate cell functions. Systems biology uses mathematical modeling and computer-based numerical simulations in order to understand emergent properties of these systems. This chapter describes the approaches to define kinetic models to simulate biochemical pathways dynamics. It deals with three main steps: the definition of the system's structure, the mathematical formulation to reproduce the time evolution and the parameter estimation to find the set of parameter values such that the model behavior fits the experimental data.