Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

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 (Δ f G′°) and reaction (Δ r G′°) in biochemical systems. Gibbs free energy contribution values were estimated for 74 di...

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Published in:Biophysical journal 2008-08, Vol.95 (3), p.1487-1499
Main Authors: Jankowski, Matthew D., Henry, Christopher S., Broadbelt, Linda J., Hatzimanikatis, Vassily
Format: Article
Language:English
Subjects:
Biochemistry
Bioenergetics
Chemical compounds
Chemical reactions
Computer Simulation
Estimating
Genomes
Gibbs free energy
Mathematical models
Models, Biological
Molecular biology
Proteome - metabolism
Signal Transduction - physiology
Standard error
Thermodynamics
Training
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cited_by cdi_FETCH-LOGICAL-c583t-ba851329d1312f68196166291a5d8e461cac52014655c8c0274237ac176100973
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creator Jankowski, Matthew D.
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Hatzimanikatis, Vassily
description 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 (Δ f G′°) and reaction (Δ r G′°) 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 Δ r G′° and Δ f G′° 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 Δ r G′° and Δ f G′° 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.
doi_str_mv 10.1529/biophysj.107.124784
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subjects Biochemistry
Bioenergetics
Chemical compounds
Chemical reactions
Computer Simulation
Estimating
Genomes
Gibbs free energy
Mathematical models
Models, Biological
Molecular biology
Proteome - metabolism
Signal Transduction - physiology
Standard error
Thermodynamics
Training
title Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
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