{
  "abstract": "Summary\n\nWe present RAFA, a C++ command-line tool for RNA all-atom structure reconstruction from sparse or partial coordinates. RAFA targets settings in which coarse-grained modelling, low-resolution fitting, or partial experimental interpretation provides RNA anchor atoms but not a complete atomic model. The method retrieves experimentally observed 3-5 nt all-atom RNA fragments, fits them to local anchors, combines overlapping fragment-derived coordinate estimates by weighted consensus, and routes sparse and rich inputs through distinct reconstruction paths. In an independent RNA3DB train/test evaluation, no library-test pair exceeded 80% global sequence identity. RAFA achieved lower all-atom root-mean-square deviation (RMSD) values than Arena in 73.3% of target-mode comparisons, with the largest gains in input modes with the fewest structural constraints.Availability and implementation\n\nRAFA is available at https://github.com/wangleiofficial/RAFA and archived at https://doi.org/10.5281/zenodo.20951205.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.",
    "School of Software Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.",
    "Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China."
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Lei Wang",
      "orcid": "0000-0002-0168-9730"
    },
    {
      "affs": [
        2
      ],
      "name": "Zilu Zeng"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/131tnvvqf8fb4.bib",
  "cited_by": 0,
  "doi": "10.1093/bioinformatics/btag746",
  "fulltext_url": "https://europepmc.org/articles/PMC13677064",
  "id": "131tnvvqf8fb4",
  "issns": [
    "1367-4803",
    "1367-4811"
  ],
  "landing_url": "https://europepmc.org/article/MED/42836828",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|RNA and protein synthesis mechanisms"
    ]
  ],
  "openalex": "W7220661481",
  "pdf_url": "https://europepmc.org/articles/PMC13677064?pdf=render",
  "pmcid": "PMC13677064",
  "pmid": "42836828",
  "published": "2026-10-01",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/131tnvvqf8fb4.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:10Z",
      "native_id": "MED:42836828",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42836828"
    },
    {
      "first_seen": "2026-10-30T12:19:38Z",
      "native_id": "10.1093/bioinformatics/btag746",
      "source": "crossref",
      "url": "https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btag746/8869022"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|RNA and protein synthesis mechanisms",
      "subfield": "molecular-biology"
    }
  ],
  "title": "RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.",
  "title_text": "RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:38Z",
  "url": "https://research.draconitic.com/paper/131tnvvqf8fb4",
  "venue": "Bioinformatics (Oxford, England)",
  "versions": []
}