eQuilibrator 3.0: a database solution for thermodynamic constant estimation

Journal Article · 28 November 2021 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkab1106 · OSTI ID:1833443

Beber, Moritz E. ^[1]; Gollub, Mattia G.  ^[2]; Mozaffari, Dana ^[3]; Shebek, Kevin M. ^[4]; Flamholz, Avi I. ^[5]; Milo, Ron ^[6]; Noor, Elad  ^[6]

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1. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark, Unseen Biometrics ApS, Fruebjergvej 3, 2100 København Ø, Denmark
2. Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel 4058, Switzerland
3. Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel 4058, Switzerland, Institute of Chemical Sciences and Engineering, EPFL, Lausanne 1015, Switzerland
4. Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
5. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
6. Department of Plant and Environmental Sciences, Weizmann Institute of Science, Herzl 234, Rehovot 7610001, Israel

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.

• Research Organization: Northwestern Univ., Evanston, IL (United States)
• Sponsoring Organization: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0018249
• OSTI ID: 1833443
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 50; ISSN 0305-1048
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United Kingdom
• Language: English