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Updated: Jul 11, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python
Jorge Carrasco Muriel1,2, Christopher Long3, Nikolaus Sonnenschein1
1Department of Biotechnology and Biomedicine, Technical University of Denmark , Kongens Lyngby, Denmark.
Importance:
The metabolism of biological cells is an intricate network of reactions that interconvert chemical compounds, gathering energy, and using that energy to grow. The static analysis of these metabolic networks can be turned into a computational model that can efficiently output the distribution of fluxes in the network. With the inclusion of enzymes in the network, we can also interpret the role and concentrations of the metabolic proteins. However, the models and the experimental data often clash, resulting in a network that cannot grow. Here, we tackle this situation with a suite of relaxation algorithms in a package called geckopy. Geckopy also integrates with other software to allow for adding thermodynamic and metabolomic constraints. In addition, to ensure that enzyme-constrained models follow the community standards, a format for the proteins is postulated. We hope that the package and algorithms presented here will be useful for the constraint-based modeling community.
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