ArticleNucleic acids research2022
eQuilibrator 3.0: a database solution for thermodynamic constant estimation.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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88 citing papers in PubMed.
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- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- Metabolic engineering of Corynebacterium glutamicum for high-yield de novo biosynthesis of 5-aminovaleramide, a promising bio-based monomer.Microbial cell factories · 2026Article
- COBRA-k: A powerful framework bridging constraint-based and kinetic metabolic modeling.Science advances · 2026Article
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- A Multi-Functional Heterogeneous Biocatalyst for the Oxygen-Free Oxidative Condensation of Primary Alcohols into β‑Hydroxy Acids.ACS catalysis · 2026Article
- High yield production of 3-hydroxypropionic acid using Issatchenkia orientalis.Nature communications · 2026Article
28 more citing papers are in PubMed but not listed here.
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts around 1,000 distinct monthly users, its design could not accommodate larger compound databases and it lacked a scalable Application Programming Interface (API) for integration into other tools developed by the systems biology community. Here, we report on the recent updates to the database as well as the addition of a new Python-based interface to eQuilibrator that adds many new features such as a 100-fold larger compound database, the ability to add novel compounds, improvements in speed and memory use, and correction for Mg2+ ion concentrations. Moreover, the new interface can compute the covariance matrix of the uncertainty between estimates, for which we show the advantages and describe the application in metabolic modelling. We foresee that these improvements will make thermodynamic modelling more accessible and facilitate the integration of eQuilibrator into other software platforms.
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