Abstract
BackgroundWhile the theory of enzyme kinetics is fundamental to analyzing and simulating biochemical systems, the derivation of rate equations for complex mechanisms for enzyme-catalyzed reactions is cumbersome and error prone. Therefore, a number of algorithms and related computer programs have been developed to assist in such derivations. Yet although a number of algorithms, programs, and software packages are reported in the literature, one or more significant limitation is associated with each of these tools. Furthermore, none is freely available for download and use by the community.ResultsWe have implemented an algorithm based on the schematic method of King and Altman (KA) that employs the topological theory of linear graphs for systematic generation of valid reaction patterns in a GUI-based stand-alone computer program called KAPattern. The underlying algorithm allows for the assumption steady-state, rapid equilibrium-binding, and/or irreversibility for individual steps in catalytic mechanisms. The program can automatically generate MathML and MATLAB output files that users can easily incorporate into simulation programs.ConclusionA computer program, called KAPattern, for generating rate equations for complex enzyme system is a freely available and can be accessed at .
Highlights
While the theory of enzyme kinetics is fundamental to analyzing and simulating biochemical systems, the derivation of rate equations for complex mechanisms for enzymecatalyzed reactions is cumbersome and error prone
The rate equations for a given discrete-state reaction mechanism can be derived by solving a system of simultaneous nonlinear algebraic equations that result from the steady-state expressions for the concentrations of all of the enzyme intermediates
We present here a simple, stand-alone computer program written in MATLAB Graphical User Interface (GUI), called KAPattern, for generating rate equations in complex enzyme systems
Summary
Generating rate equations for complex enzyme systems by a computer-assisted systematic method. Address: Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA. Published: 4 August 2009 BMC Bioinformatics 2009, 10:238 doi:10.1186/1471-2105-10-238
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