{
  "abstract": "Designing RNA molecules that bind to target protein structures requires generating both an RNA conformation and its bound complex geometry, without assuming a predefined binding site. Existing approaches generally model these coupled processes within a unified representation, entangling RNA conformation generation with protein-relative placement. In this work, we introduce RiboBridge, a structure-first framework that separates RNA conformational generation from protein--RNA assembly through cross-frame interaction geometry. RiboBridge first proposes multiple candidate RNA-binding interfaces on the protein surface, generates canonical RNA conformations within a pretrained RNA structural latent space (RiboSphere), and then predicts protein--RNA interaction constraints to bridge the independently defined RNA and protein coordinate frames. The resulting interaction geometry is converted into a geometrically consistent protein-relative pose through rigid placement. We evaluate RiboBridge on a temporally split, sequence-filtered, and redundancy-controlled benchmark of 124 protein--RNA complexes. Under post-hoc interface-correspondence evaluation, where native information is used only after generation to select among already generated predicted-pocket candidates, RiboBridge achieves the highest fNAT and DockQ and the lowest interface and ligand RMSDs among compared methods. Component ablations and stage-wise diagnostics further characterize the contributions of RNA conformational generation, interaction prediction, and rigid placement, identifying the main sources of complex-recovery error.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2610.30668",
  "author_total": 8,
  "authors": [
    {
      "name": "Zhou Zhang"
    },
    {
      "name": "Hanqun Cao"
    },
    {
      "name": "Minghao Sun"
    },
    {
      "name": "Odin Zhang"
    },
    {
      "name": "Yang Zhang"
    },
    {
      "name": "Pheng Ann Heng"
    },
    {
      "name": "Wujun Li"
    },
    {
      "name": "Tianfan Fu"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7nsc2psnnatcd.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2610.30668",
  "fulltext_url": null,
  "id": "7nsc2psnnatcd",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2610.30668",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cs.LG"
    ],
    [
      "arxiv",
      "q-bio.BM"
    ],
    [
      "openalex",
      "1312|RNA and protein synthesis mechanisms"
    ]
  ],
  "openalex": "W7223308328",
  "pdf_url": "https://arxiv.org/pdf/2610.30668",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-22",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/7nsc2psnnatcd.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:34:38Z",
      "native_id": "2610.30668",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2610.30668"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "arxiv:q-bio.BM",
      "subfield": "biophysics"
    }
  ],
  "title": "RiboBridge: protein-conditioned de novo RNA binder structure design",
  "title_text": "RiboBridge: protein-conditioned de novo RNA binder structure design",
  "type": "preprint",
  "updated_at": "2026-10-30T12:34:38Z",
  "url": "https://research.draconitic.com/paper/7nsc2psnnatcd",
  "venue": "arXiv",
  "versions": []
}