ArticlePLoS computational biology2013
Consistent estimation of Gibbs energy using component contributions.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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Who cites it
136 citing papers in PubMed.
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- Pathway thermodynamic analysis postulates change in glutamate metabolism as a key factor in modulating immune responses.Immunometabolism (Cobham, Surrey) · 2026Article
- Identification of overoxidizing and non-overoxidizing NAD-dependent methanol dehydrogenases and implications for synthetic methylotrophy.Nature communications · 2025Article
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- A compact model of Escherichia coli core and biosynthetic metabolism.PLoS computational biology · 2025Article
- Complex Kinetic Models Predict β-Carotene Production and Reveal Flux Limitations in RecombinantACS synthetic biology · 2025Article
- The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions.ACS synthetic biology · 2025Review
- Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways.PLoS computational biology · 2025Article
- One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle.Nature microbiology · 2025Article
76 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism.
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