{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "BioSystems Engineering and Control (BiSECt) Lab, Institute of Technology Madras, Chennai, Tamil Nadu, India; The Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, Tamil Nadu, India; Department of Data Science and AI, Wadhwani School of Data Science and AI, IIT Madras, Chennai, Tamil Nadu, India. Electronic address: spavaniitm@smail.iitm.ac.in."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Pavan Kumar"
    },
    {
      "name": "Nirav Pravinbhai Bhatt"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/95zvbmvz41m9q.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104890",
  "fulltext_url": "https://europepmc.org/articles/PMC13675701",
  "id": "95zvbmvz41m9q",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://europepmc.org/article/MED/42848515",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Microbial Metabolic Engineering and Bioproduction"
    ]
  ],
  "openalex": "W7221045725",
  "pdf_url": "https://europepmc.org/articles/PMC13675701?pdf=render",
  "pmcid": "PMC13675701",
  "pmid": "42848515",
  "published": "2026-10-08",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/95zvbmvz41m9q.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:02Z",
      "native_id": "MED:42848515",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42848515"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Microbial Metabolic Engineering and Bioproduction",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.",
  "title_text": "Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:02Z",
  "url": "https://research.draconitic.com/paper/95zvbmvz41m9q",
  "venue": "STAR protocols",
  "versions": []
}