{
  "abstract": "AlphaFold 3 (AF3) predicts protein ligand complexes, but the utility of its confidence scores for drug discovery remains unclear. We benchmarked AF3 interaction scores against BANDOCK+, an experimentally informed approach, using approved drugs and human protein libraries. AF3 ipTM achieved slightly higher observed aggregate disease ranking scores in a matched 1,103 protein comparison, with performance varying among individual indications. BANDOCK+ enabled substantially broader protein coverage using a computationally less demanding approach, including a 20,158 protein reference library. These findings highlight the potential of AF3 confidence scores for computational drug discovery and the tradeoffs between predictive performance and scalability.",
  "abstract_shown": true,
  "affiliations": [
    "University at Buffalo"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "R. Akabari"
    },
    {
      "name": "W. Mangione"
    },
    {
      "name": "Z. Falls"
    },
    {
      "affs": [
        0
      ],
      "name": "R. Samudrala"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/330afbyb5p0rx.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.19.757941",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.19.757941v1.full",
  "id": "330afbyb5p0rx",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.19.757941v1",
  "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",
      "bioinformatics"
    ],
    [
      "openalex",
      "1703|Computational Drug Discovery Methods"
    ]
  ],
  "openalex": "W7223006681",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.19.757941v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-19",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/330afbyb5p0rx.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:28:38Z",
      "native_id": "10.64898/2026.10.19.757941",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.19.757941v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Proteome scale drug prioritization from AlphaFold 3 interaction confidence",
  "title_text": "Proteome scale drug prioritization from AlphaFold 3 interaction confidence",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:10Z",
  "url": "https://research.draconitic.com/paper/330afbyb5p0rx",
  "venue": "bioRxiv",
  "versions": []
}