Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Flamholz, Avi, Noor, Elad, Bar-Even, Arren, Milo, Ron
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
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
_version_ 1782219790977335296
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
work_keys_str_mv AT flamholzavi equilibratorthebiochemicalthermodynamicscalculator
AT noorelad equilibratorthebiochemicalthermodynamicscalculator
AT barevenarren equilibratorthebiochemicalthermodynamicscalculator
AT miloron equilibratorthebiochemicalthermodynamicscalculator