Work

Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA

Year: 2026

Type: article

Abstract: Thermodynamically infeasible cycles violate the second law of thermodynamics but are permitted by stoichiometric flux analysis. Here, we present a protocol for the construction and analysis of metabolic networks using ThermOptCOBRA, a MATLAB extension of the COBRA Toolbox. We describe steps for enumerating cycles (ThermOptEnumerator), determining feasible directions and blocked reactions (ThermOptCC), and building thermodynamically consistent context-specific models using omics data (ThermOptiCS). We then detail procedures for removing loops or sample loopless flux distributions (ThermOptFlux/ADSB-ThermOptFlux). For complete details on the use and execution of this protocol, please refer to Kumar and Bhatt. 1 1. Kumar S, P. ∙ Bhatt, N.P. ThermOptCobra: Thermodynamically optimal construction and analysis of metabolic networks for reliable phenotype predictions iScience. 2025; 28 , 113005 Full Text Full Text (PDF) Scopus (3) Google Scholar

Source: STAR Protocols

DOI: 10.1016/j.xpro.2026.104890

Authors: Pavan Kumar, Nirav Pravinbhai Bhatt

Institution: Indian Institute of Technology Madras

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,550

Funder: Indian Institute of Technology Madras