{
  "abstract": "We present SMartini, an automated pipeline for deriving Martini 3 coarse-grained force-field parameters for arbitrary small molecules. Starting from a molecular structure or a SMILES string, the pipeline maps the all-atom molecule onto a coarse-grained bead representation and automatically fits both bonded and non-bonded parameters. Bonded parameters are obtained via Boltzmann inversion of atomistic molecular dynamics trajectories; successive rounds of coarse-grained simulation and distribution-matching updates then refine these estimates until the coarse-grained conformational ensemble reproduces the all-atom reference within tolerance. We validate the pipeline on a diverse set of small molecules including drug-like compounds, metabolites, and cofactors. Implemented as a modular sequence of scripts that can be orchestrated on high-performance computing clusters, SMartini makes automated parametrization of large ligand libraries practical and reduces the manual effort required for coarse-grained model development, enabling high-throughput coarse-grained simulations of protein--ligand systems within the Martini 3 ecosystem",
  "abstract_shown": true,
  "affiliations": [
    "Arizona State University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "D. Yangaliev"
    },
    {
      "name": "S. B. Ozkan"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b7r44cgd2sqxs.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.29.755481",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.29.755481v1.full",
  "id": "b7r44cgd2sqxs",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.29.755481v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7216411333",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.29.755481v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-29",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b7r44cgd2sqxs.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:44Z",
      "native_id": "10.64898/2026.09.29.755481",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.29.755481v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "SMartini: automated small molecule parametrization for Martini 3 force field",
  "title_text": "SMartini: automated small molecule parametrization for Martini 3 force field",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:44Z",
  "url": "https://research.draconitic.com/paper/b7r44cgd2sqxs",
  "venue": "bioRxiv",
  "versions": []
}