eQuilibrator--the biochemical thermodynamics calculator
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No Canadian affiliation. An affiliation-only frame — the usual design — would never have seen this work. It is one of the works that make the case for inverting the frame.
Machine scores (provisional)
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- Teacher spread
- 0.256 · how far apart the two teachers sit on this one work
- Validation status
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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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
The record
- Venue
- Nucleic Acids Research
- Topic
- Microbial Metabolic Engineering and Bioproduction
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- Azrieli FoundationIsrael Academy of Sciences and Humanities
- Keywords
- Gibbs free energyCalculatorSimple (philosophy)Interface (matter)ThermodynamicsComputer scienceSource codeStatistical physicsCode (set theory)PhysicsProgramming languageSet (abstract data type)
- Has abstract in OpenAlex
- yes