Group contribution method for thermodynamic analysis of complex metabolic networks |
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Authors: | Jankowski Matthew D Henry Christopher S Broadbelt Linda J Hatzimanikatis Vassily |
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Institution: | * Mayo Clinic, Rochester, Minnesota 55905 † Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439 ‡ Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois 60208 § Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland |
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Abstract: | A new, to our knowledge, group contribution method based on the group contribution method of Mavrovouniotis is introduced for estimating the standard Gibbs free energy of formation (ΔfG′°) and reaction (ΔrG′°) in biochemical systems. Gibbs free energy contribution values were estimated for 74 distinct molecular substructures and 11 interaction factors using multiple linear regression against a training set of 645 reactions and 224 compounds. The standard error for the fitted values was 1.90 kcal/mol. Cross-validation analysis was utilized to determine the accuracy of the methodology in estimating ΔrG′° and ΔfG′° for reactions and compounds not included in the training set, and based on the results of the cross-validation, the standard error involved in these estimations is 2.22 kcal/mol. This group contribution method is demonstrated to be capable of estimating ΔrG′° and ΔfG′° for the majority of the biochemical compounds and reactions found in the iJR904 and iAF1260 genome-scale metabolic models of Escherichia coli and in the Kyoto Encyclopedia of Genes and Genomes and University of Minnesota Biocatalysis and Biodegradation Database. A web-based implementation of this new group contribution method is available free at http://sparta.chem-eng.northwestern.edu/cgi-bin/GCM/WebGCM.cgi. |
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