{
  "abstract": "Learning molecular models of RNA requires simulation data that capture conformational variability and provide consistent physical training signals. Here, we introduce mdRNAcat, a curated dataset of all-atom molecular dynamics (MD) simulations of 48 RNA systems selected to promote sequence diversity. Each system is simulated using replica-exchange with solute scaling (REST2), with 32 Hamiltonian states and production lengths of 200-300 ns per state. The dataset provides atomic coordinates, instantaneous forces, and forces reevaluated under the unscaled reference Hamiltonian, together with structural annotations and replica-exchange metadata. Coordinates and forces are available at 1 ps intervals for the reference state and 100 ps intervals across all states in a standardized HDF5 format. We characterize conformational sampling, exchange behavior, base pairing, and sugar-pucker distributions to document the properties of the simulated ensembles. mdRNAcat provides a reusable resource for developing and evaluating data-driven RNA models, including coarse-grained force fields.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2610.35204",
  "author_total": 6,
  "authors": [
    {
      "name": "Anton E. Dorn"
    },
    {
      "name": "Emile de Bruyn"
    },
    {
      "name": "Fabrice von der Lehr"
    },
    {
      "name": "Philipp Knechtges"
    },
    {
      "name": "Stefan Kesselheim"
    },
    {
      "name": "Alexander Schug"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/11hvhbk8msytm.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2610.35204",
  "fulltext_url": null,
  "id": "11hvhbk8msytm",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2610.35204",
  "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.LG"
    ],
    [
      "arxiv",
      "physics.bio-ph"
    ],
    [
      "arxiv",
      "q-bio.BM"
    ],
    [
      "openalex",
      "1312|RNA and protein synthesis mechanisms"
    ]
  ],
  "openalex": "W7223971989",
  "pdf_url": "https://arxiv.org/pdf/2610.35204",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/11hvhbk8msytm.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:35:50Z",
      "native_id": "2610.35204",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2610.35204"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "arxiv:q-bio.BM",
      "subfield": "biophysics"
    },
    {
      "field": "physics",
      "origin": "arxiv:physics.bio-ph",
      "subfield": "biological-medical"
    }
  ],
  "title": "mdRNAcat: A Molecular Dynamics RNA Catalog of REST2 Conformational Ensembles",
  "title_text": "mdRNAcat: A Molecular Dynamics RNA Catalog of REST2 Conformational Ensembles",
  "type": "preprint",
  "updated_at": "2026-10-30T12:35:56Z",
  "url": "https://research.draconitic.com/paper/11hvhbk8msytm",
  "venue": "arXiv",
  "versions": []
}