ArticleBiophysical journal2008
Group contribution method for thermodynamic analysis of complex metabolic networks.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
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153 citing papers in PubMed.
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- The minimum energy required to build a cell.Scientific reports · 2024Article
- Rational strain design with minimal phenotype perturbation.Nature communications · 2024Article
- Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states.Nature catalysis · 2024Article
- Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution.Nature communications · 2023Article
- Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.PLoS computational biology · 2023Article
- Unravelling the hidden power of esterases for biomanufacturing of short-chain esters.Scientific reports · 2023Article
- Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants.PLoS computational biology · 2023Article
- Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations.Nature communications · 2023Article
- Investigating the Unique Ability ofmSystems · 2023Article
- Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production inACS synthetic biology · 2022Article
93 more citing papers are in PubMed but not listed here.
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4 authors.
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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 (Delta(f)G'(o)) and reaction (Delta(r)G'(o)) 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 Delta(r)G'(o) and Delta(f)G'(o) 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 Delta(r)G'(o) and Delta(f)G'(o) 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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