{
  "abstract": "Virtual screening aims to prioritize active compounds from large chemical libraries within a limited experimental budget. When applying Boltz-2 to virtual screening, a key challenge is how to use limited experimental data from the target assay to improve the prioritization of active compounds. We investigated whether fine-tuning the Boltz-2 affinity heads with a small number of binary activity labels could improve early enrichment of active compounds in hit discovery. We compared fine-tuning with 40-300 labels in a retrospective evaluation on eight MF-PCBA targets. With 300 activity measurements, fine-tuning increased the number of actives in the top 1% by a geometric mean of 1.77-fold across the eight targets and improved average precision (AP) by 2.14-fold relative to the control without fine-tuning. We also investigated whether rescoring a subset of candidates could retain the improvement in hit recovery by reranking only the top-ranked Boltz-2 candidates with the fine-tuned head. Restricting rescoring to approximately 10% of the evaluation set retained hit recovery comparable to full rescoring. These findings show that affinity-head fine-tuning with limited activity labels improves early enrichment with Boltz-2 and that this benefit can be retained when rescoring a restricted set of candidates.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2609.24302",
  "author_total": 2,
  "authors": [
    {
      "name": "Kairi Furui"
    },
    {
      "name": "Masahito Ohue"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9zrm5axxp4xz2.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2609.24302",
  "fulltext_url": null,
  "id": "9zrm5axxp4xz2",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2609.24302",
  "language": null,
  "licence": "LicenseRef-arXiv-nonexclusive-1.0",
  "licence_label": "arXiv licence",
  "licence_source": "article",
  "licence_url": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cs.AI"
    ],
    [
      "arxiv",
      "cs.LG"
    ],
    [
      "arxiv",
      "q-bio.BM"
    ],
    [
      "arxiv",
      "q-bio.QM"
    ],
    [
      "openalex",
      "1703|Computational Drug Discovery Methods"
    ]
  ],
  "openalex": "W7214012071",
  "pdf_url": "https://arxiv.org/pdf/2609.24302",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9zrm5axxp4xz2.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:23:28Z",
      "native_id": "2609.24302",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2609.24302"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "arxiv:q-bio.BM",
      "subfield": "biophysics"
    },
    {
      "field": "biology",
      "origin": "arxiv:q-bio.QM",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Adapting Boltz-2 with limited experimental activity data improves early enrichment in virtual screening",
  "title_text": "Adapting Boltz-2 with limited experimental activity data improves early enrichment in virtual screening",
  "type": "preprint",
  "updated_at": "2026-10-30T12:23:28Z",
  "url": "https://research.draconitic.com/paper/9zrm5axxp4xz2",
  "venue": "arXiv",
  "versions": []
}