Consistent Estimation of Gibbs Energy Using Component Contributions
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 soluti...
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Public Library of Science
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708888/ |
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pubmed-37088882013-07-19 Consistent Estimation of Gibbs Energy Using Component Contributions Noor, Elad Haraldsdóttir, Hulda S. Milo, Ron Fleming, Ronan M. T. Research Article 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. Public Library of Science 2013-07-11 /pmc/articles/PMC3708888/ /pubmed/23874165 http://dx.doi.org/10.1371/journal.pcbi.1003098 Text en © 2013 Noor et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Noor, Elad Haraldsdóttir, Hulda S. Milo, Ron Fleming, Ronan M. T. |
| spellingShingle |
Noor, Elad Haraldsdóttir, Hulda S. Milo, Ron Fleming, Ronan M. T. Consistent Estimation of Gibbs Energy Using Component Contributions |
| author_facet |
Noor, Elad Haraldsdóttir, Hulda S. Milo, Ron Fleming, Ronan M. T. |
| author_sort |
Noor, Elad |
| title |
Consistent Estimation of Gibbs Energy Using Component Contributions |
| title_short |
Consistent Estimation of Gibbs Energy Using Component Contributions |
| title_full |
Consistent Estimation of Gibbs Energy Using Component Contributions |
| title_fullStr |
Consistent Estimation of Gibbs Energy Using Component Contributions |
| title_full_unstemmed |
Consistent Estimation of Gibbs Energy Using Component Contributions |
| title_sort |
consistent estimation of gibbs energy using component contributions |
| description |
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. |
| publisher |
Public Library of Science |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708888/ |
| _version_ |
1611994190536769536 |