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eQuilibrator 3.0: a database solution for thermodynamic constant estimation

Authors :: Kevin M. Shebek
Elad Noor
Mattia G. Gollub
Moritz Emanuel Beber
Dana Mozaffari
Avi I. Flamholz
Ron Milo
Source :: Nucleic Acids Research, Beber, M E, Gollub, M G, Mozaffari, D, Shebek, K M, Flamholz, A I, Milo, R & Noor, E 2022, ' eQuilibrator 3.0: a database solution for thermodynamic constant estimation ', Nucleic Acids Research, vol. 50, no. D1, pp. D603–D609 . https://doi.org/10.1093/nar/gkab1106, Nucleic Acids Research, 50 (D1)
Publication Year :: 2021
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.<br />Nucleic Acids Research, 50 (D1)<br />ISSN:1362-4962<br />ISSN:0301-5610