{
  "abstract": "AlphaFold 3 (AF3) models RNA and protein-RNA complexes, but when its predictions and confidence metrics can be trusted is unclear. We evaluated AF3 on more than 1,300 protein-RNA complexes and about 270 RNA-only systems, and compared post-cutoff RNAs with pre-cutoff candidates selected by sequence and fold similarity. On structurally novel RNAs, AF3 largely preserves the protein fold, while RNA-fold and interface accuracy drop sharply with little change in predicted RNA confidence score. Input ablations show that protein alignments and templates from RNA-bound proteins govern complex assembly, whereas RNA alignments matter most for single-chain and long RNAs. The most frequent failed interface retains protein-side contacts but places an often-misfolded RNA in the wrong pose. RNA interface confidence only partly distinguishes this error from correct placements. Against CLIP-seq, SELEX and RNAcompete motifs, AF3 usually places the protein against the experimentally observed motif-bearing RNA segment, even where the interface fails, but often not in the native pose. In protein-RNA complexes released in 2026, a score combining AF3 confidence with RNA familiarity and template use ranked RNA chains with accurate folds and correctly placed interfaces better than AF3's ranking score.",
  "abstract_shown": true,
  "affiliations": [
    "University of Freiburg"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "name": "I. K. Tennie"
    },
    {
      "name": "M. Uhl"
    },
    {
      "name": "J. K. H. Franke"
    },
    {
      "name": "R. Backofen"
    },
    {
      "affs": [
        0
      ],
      "name": "F. Runge"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/77cxfpr23mxbr.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.02.763690",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763690v1.full",
  "id": "77cxfpr23mxbr",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763690v1",
  "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": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763690v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/77cxfpr23mxbr.ris",
  "sources": [
    {
      "first_seen": "2026-11-05T00:21:52Z",
      "native_id": "10.64898/2026.11.02.763690",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.11.02.763690v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces",
  "title_text": "AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces",
  "type": "preprint",
  "updated_at": "2026-11-06T00:21:39Z",
  "url": "https://research.draconitic.com/paper/77cxfpr23mxbr",
  "venue": "bioRxiv",
  "versions": []
}