eQuilibrator—the biochemical thermodynamics calculator
By Avi I. Flamholz, Elad Noor, A. Bar‐Even, Ron Milo. Nucleic Acids Res., 2011
556 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Physical and Theoretical Chemistry
View Paper: https://www.semanticscholar.org/paper/39809fbd9bbe9c93cea1b14699ad9477df5b5c1f
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In Molecular Biology
- Adam M. Feist
- D. McCloskey
- Bernhard O. Palsson
- David Baker
- Barry L. Stoddard
- Jasmine L. Gallaher
- A. Bar‐Even
- Jay D. Keasling
In Physical and Theoretical Chemistry
Citations in the corpus
- Computational protein design enables a novel one-carbon assimilation pathway (2015, background): “coli cytoplasmic conditions, the ATP-dependent formation of formyl-CoA can have a ΔrG′° as low as −4 kcal/mol (12, 13).”
- Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli (2013, methodology): “…loops that violate energy balance (Ederer and Gilles, 2007; Fleming et al , 2009), by refining reaction directionality, and by defining allowable flux ranges via calculation of the in vivo change of Gibbs free energyof reactions (Ku¨mmel et al , 2006; Henry et al , 2007; Flamholz et al , 2012).”