Kinetic modeling and fitting software for interconnected reaction schemes: VisKin.
Reaction kinetics for complex, highly interconnected kinetic schemes are modeled using analytical solutions to a system of ordinary differential equations. The algorithm employs standard linear algebra methods that are implemented using MatLab functions in a Visual Basic interface. A graphical user interface for simple entry of reaction schemes facilitates comparison of a variety of reaction schemes. To ensure microscopic balance, graph theory algorithms are used to determine violations of thermodynamic cycle constraints. Analytical solutions based on linear differential equations result in fast comparisons of first order kinetic rates and amplitudes as a function of changing ligand concentrations. For analysis of higher order kinetics, we also implemented a solution using numerical integration. To determine rate constants from experimental data, fitting algorithms that adjust rate constants to fit the model to imported data were implemented using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno methods. We have included the ability to carry out global fitting of data sets obtained at varying ligand concentrations. These tools are combined in a single package, which we have dubbed VisKin, to guide and analyze kinetic experiments. The software is available online for use on PCs.
Zhang
Xuan
X
Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
Andrews
Jared N
JN
Pedersen
Steen E
SE
D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D008956:Models, Chemical; D012984:Software; D012985:Software Design