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Published (Version of record)CC BY-NC V3.0, Open Access
Journal article
eQuilibrator: the biochemical thermodynamics calculator
Nucleic Acids Research, Vol.40(D1), pp.D770-D775
Jan/2012
Abstract
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.
Details
- Title
- eQuilibrator; the biochemical thermodynamics calculator
- Creators
- Avi Flamholz (null)Elad Noor (null) - 972WIS_INST___110Arren Bar-Even (null) - 972WIS_INST___110Ron Milo (null) - 972WIS_INST___110
- Resource Type
- Journal article
- Publication Details
- Nucleic Acids Research, Vol.40(D1), pp.D770-D775; Jan/2012
- Number of pages
- 6
- Language
- English
- DOI
- https://doi.org/10.1093/nar/gkr874
- Grant note
- The authors would like to thank Jaime Prilusky and Shay Cohen-Laor for technical assistance in setting up eQuilibrator and Wolfram Liebermeister, Robert Goldberg, Brian Kernighan, Niv Antonovsky, Lior Zelcbuch, Guy Polturak, Yaniv Lubling, Tomer Shlomi, Naama Tepper, Ido Shani and Avigail Hurvitz-Prinz for helpful comments on the site and the article. FUNDING European Research Council (grant 260392 - SYMPAC); Azrieli Foundation (to E.N.). Adams Fellowship Program of the Israel Academy of Sciences and Humanities (to A.B.E.); ERC (260392 - SYMPAC) (to R.M.); Anna and Maurice Boukstein career development chair (to R.M.). Funding for open access charge: ERC._ALMAME_DELIMITER_
- Record Identifier
- 993265322103596
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