eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions. Estimation of thermodynamic parameters (ΔrG and ΔfG) elucidates how much energy is required to drive a particular biochemical reaction and in which direction the reaction will flow in particular cellular conditions 1 2.
Because experimental measurement of the free energy of formation (ΔfG°) of compounds is technically challenging, the vast majority of known metabolites have not been thermodynamically characterized. eQuilibrator uses a well-studied approximation of ΔfG called group contribution 3 4 5, enabling thermodynamic analysis of many biochemical reactions and pathways.
Currently, eQuilibrator can provide estimates for many compounds in the KEGG database 7 (about 4500). Individual compounds and enzymes can be searched for by their common names (“water”, “glucosamine”, “hexokinase”), and reactions can be entered in a simple, free-text format (“ribulose bisphosphate + CO2 + water => 2 3-phosphoglycerate”) that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations - to help explore the thermodynamic landscape of a biochemical reaction.
Implementation of eQuilibrator¶
eQuilibrator makes heavy use of open source libraries and frameworks and is open-source itself. You can find the eQuilibrator source code on our GitLab repository called equilibrator.
All thermodynamic data presented by eQuilibrator was generated using the Component Contribution method [DOI: 10.1371/journal.pcbi.1003098] 6 which was implemented also in Python and is open-source as well. You can find the source code on our GitHub repository called component-contribution.
Avi Flamholz, Elad Noor, Ron Milo and Arren Bar-Even designed the eQuilibrator interface
Avi Flamholz and Elad Noor implemented eQuilibrator
Elad Noor, Avi Flamholz, Hulda Haraldsdóttir, Arren Bar-Even and Ron Milo designed and tuned eQuilibrator’s version of the component contribution
Alberty, “Thermodynamics of biochemical reactions” (Hoboken N.J.: Wiley-Interscience, 2003)
Alberty, “Biochemical Thermodynamics” (Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006)
Mavrovouniotis, “Estimation of standard Gibbs energy changes of biotransformations” The Journal of Biological Chemistry (1991) 266(22):14440-14445
Jankowski et al., “Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks” Biophysical Journal (2008) 95(3):1487-1499
Noor, A. Bar-Even, A. Flamholz, Y. Lubling, D. Davidi, R. Milo, “An integrated open framework for thermodynamics of reactions that combines accuracy and coverage” Bioinformatics (2012) 28:2037-2044
Noor, H. S. Haraldsdóttir, R. Milo, R. M. T. Fleming, “Consistent Estimation of Gibbs Energy Using Component Contributions” PLoS Comput Biol (2013) 9:e1003098
Kanehisa, S. Goto, “KEGG: Kyoto Encyclopedia of Genes and Genomes” Nucleic Acids Research (2000) 28(1):27-30