EQuilibrator 3.0: a database solution for thermodynamic constant estimation. Issue Volume 50:Issue D1(2022) (29th November 2021)

• Record Type: Journal Article
• Authors: Beber, Moritz E; Gollub, Mattia G; Mozaffari, Dana; Shebek, Kevin M; Flamholz, Avi I; Milo, Ron; Noor, Elad
• Is Part Of: Nucleic acids research. Volume 50:Issue D1(2022)
• Page Start: D603
• Page End: D609
• Publication Date: 2021-11-29
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab1106
• Languages: English
• ISSNs: 0305-1048

Abstract

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 Mg 2+ 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.