{
  "abstract": "Designed binders are routinely filtered on predicted interface confidence, which reports how self-consistently a model places an interface, not where it lies. We designed 200 nanobody loops against the survivin BIR-domain groove, co-folded 196, and checked epitope contact in every predicted complex. Confidence showed no detectable association with epitope engagement ({rho} = +0.100, 95% CI -0.04 to +0.24, n = 196); its highest and lowest quartiles failed alike (odds ratio 0.97, 95% CI 0.41 to 2.26). It tracked instead the run's other confidence estimates ({rho} = +0.61). Twelve-seed replication separated two candidates the criteria had not: one reached the complete epitope in 10 of 12 runs, the other never. Across 155 predictions the top-ranked model was no better than one drawn at random from its five (P = 0.610), though only 3 of 31 failed on every model. Nothing was assayed; nb_cand_057 is an in silico candidate only.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong Univ"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "name": "C. Gately"
    },
    {
      "name": "X. Guan"
    },
    {
      "affs": [
        0
      ],
      "name": "X. Ding"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/akc0r9keqrc5w.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.04.753929",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.04.753929v1.full",
  "id": "akc0r9keqrc5w",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.04.753929v1",
  "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",
      "1312|vaccines and immunoinformatics approaches"
    ]
  ],
  "openalex": "W7221457607",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.04.753929v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-04",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/akc0r9keqrc5w.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:27:12Z",
      "native_id": "10.64898/2026.10.04.753929",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.04.753929v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Benchmarking interface confidence as a selection criterion for computational nanobody design against survivin's BIR-domain groove",
  "title_text": "Benchmarking interface confidence as a selection criterion for computational nanobody design against survivin's BIR-domain groove",
  "type": "preprint",
  "updated_at": "2026-10-30T12:27:12Z",
  "url": "https://research.draconitic.com/paper/akc0r9keqrc5w",
  "venue": "bioRxiv",
  "versions": []
}