Generating rate equations for complex enzyme systems by a computer-assisted systematic method. BMC Bioinformatics 2009 Aug 04;10:238
Date
08/06/2009Pubmed ID
19653903Pubmed Central ID
PMC2729780DOI
10.1186/1471-2105-10-238Scopus ID
2-s2.0-69049085645 (requires institutional sign-in at Scopus site) 32 CitationsAbstract
BACKGROUND: While 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.
RESULTS: We 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.
CONCLUSION: A computer program, called KAPattern, for generating rate equations for complex enzyme system is a freely available and can be accessed at http://www.biocoda.org.
Author List
Qi F, Dash RK, Han Y, Beard DAAuthor
Ranjan K. Dash PhD Professor in the Biomedical Engineering department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AlgorithmsBiocatalysis
Fumarate Hydratase
Software
Systems Biology
