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eQuilibrator—the biochemical thermodynamics calculator
The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245061/ https://www.ncbi.nlm.nih.gov/pubmed/22064852 http://dx.doi.org/10.1093/nar/gkr874 |
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author | Flamholz, Avi Noor, Elad Bar-Even, Arren Milo, Ron |
author_facet | Flamholz, Avi Noor, Elad Bar-Even, Arren Milo, Ron |
author_sort | Flamholz, Avi |
collection | PubMed |
description | The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. |
format | Online Article Text |
id | pubmed-3245061 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-32450612012-01-10 eQuilibrator—the biochemical thermodynamics calculator Flamholz, Avi Noor, Elad Bar-Even, Arren Milo, Ron Nucleic Acids Res Articles The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. Oxford University Press 2012-01 2011-11-07 /pmc/articles/PMC3245061/ /pubmed/22064852 http://dx.doi.org/10.1093/nar/gkr874 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Flamholz, Avi Noor, Elad Bar-Even, Arren Milo, Ron eQuilibrator—the biochemical thermodynamics calculator |
title | eQuilibrator—the biochemical thermodynamics calculator |
title_full | eQuilibrator—the biochemical thermodynamics calculator |
title_fullStr | eQuilibrator—the biochemical thermodynamics calculator |
title_full_unstemmed | eQuilibrator—the biochemical thermodynamics calculator |
title_short | eQuilibrator—the biochemical thermodynamics calculator |
title_sort | equilibrator—the biochemical thermodynamics calculator |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245061/ https://www.ncbi.nlm.nih.gov/pubmed/22064852 http://dx.doi.org/10.1093/nar/gkr874 |
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