{
  "abstract": "Molecular docking is widely used to predict ligand-protein interactions, but its application to transition metal complexes, particularly those containing second- and third-row elements, remains limited by the lack of explicit metal parameterization in commonly used programs such as AutoDock Vina. Here, we present a simple, practical strategy for docking heavy transition metal complexes without reparameterization: substituting the metal center with its first-row congener (e.g. Ru → Fe; Ir → Co) prior to docking. We applied this approach to a dataset of approximately 60 crystallographically characterized protein-ligand complexes containing Re, Ru, Os, Rh, Ir, Pt and Pd, and then focused on a streptavidin/avidin-biotin validation set of 18 crystallographically characterized protein-ligand complexes (4 Ru, 14 Ir) retrieved from the Protein Data Bank. The experimentally observed binding pose on the full set (rigid docking) was reproduced in 66% of cases, while for the streptavidin/avidin-biotin systems (flexible docking) the crystallography pose was fully or partially reproduced in 60% of cases (3/4 for the Ru systems and 8/14 for the Ir systems). Despite this outcome heterogeneity, the coordination geometry of the metal center and the broader protein-ligand interaction fingerprint were well preserved across the docked complexes, with a smaller perturbation observed for the Ru/Fe pair than for the Ir/Co pair, consistent with the higher pose-recovery rate obtained for the Ru systems. Overall, these results indicate that congener substitution offers a rapid, accessible route to docking second- and third-row transition metal complexes with unmodified AutoDock Vina, particularly in rigid docking, while revealing possible metal- and system-dependent limitations that should be considered when extending the strategy to other systems.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, University of Fribourg, Chemin Du Musée 9, Fribourg, Switzerland, 1700",
    "Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy, 35131"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Miroslava Nedyalkova",
      "orcid": "0000-0003-0793-3340"
    },
    {
      "affs": [
        1
      ],
      "name": "Simone Bernardotto"
    },
    {
      "affs": [
        0
      ],
      "name": "Fabio Zobi"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8xeh8p860zew9.bib",
  "cited_by": 0,
  "doi": "10.26434/chemrxiv.15009469/v1",
  "fulltext_url": null,
  "id": "8xeh8p860zew9",
  "issns": [],
  "landing_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009469/v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1703|Computational Drug Discovery Methods"
    ]
  ],
  "openalex": "W7214356825",
  "pdf_url": "https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15009469/v1",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-25",
  "publisher": "American Chemical Society (ACS)",
  "ris": "https://research.draconitic.com/paper/8xeh8p860zew9.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:21Z",
      "native_id": "10.26434/chemrxiv.15009469",
      "source": "chemrxiv",
      "url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009469/v1"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "source:chemrxiv",
      "subfield": "general"
    }
  ],
  "title": "A Congener-Substitution Strategy for Docking Heavy Metal Protein-Ligand Complexes with AutoDock Vina",
  "title_text": "A Congener-Substitution Strategy for Docking Heavy Metal Protein-Ligand Complexes with AutoDock Vina",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:21Z",
  "url": "https://research.draconitic.com/paper/8xeh8p860zew9",
  "venue": "ChemRxiv",
  "versions": []
}