{
  "abstract": "Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single representation. Here, we show that representation choice is not neutral: it fundamentally shapes the conformational organization, similarity relationships, and apparent transitions inferred from identical simulation data. To complement existing representations, we introduce Orientation features, a geometrically grounded, rotation-aware encoding of protein backbone. We compare it against common descriptions across three dynamical regimes: fast-folding proteins, large-scale domain motions, and protein-protein association. Across these systems, we find that different representations emphasize complementary aspects of conformational space, and that no single representation provides a complete picture of the underlying dynamics. To facilitate systematic comparison, we developed ManiProt, a library for efficient computation and analysis of multiple protein representations. Our results motivate a comparative, representation-aware framework for the interpretation of molecular dynamics simulations.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Giottonini Axel",
      "orcid": "0009-0000-6404-561X"
    },
    {
      "name": "Lemmin Thomas",
      "orcid": "0000-0001-5705-4964"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9gjq9bjvtnssd.bib",
  "cited_by": 0,
  "doi": "10.1038/s42004-026-02209-x",
  "fulltext_url": null,
  "id": "9gjq9bjvtnssd",
  "issns": [
    "2399-3669"
  ],
  "landing_url": "https://www.nature.com/articles/s42004-026-02209-x",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7221516205",
  "pdf_url": "https://www.nature.com/articles/s42004-026-02209-x_reference.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-12",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/9gjq9bjvtnssd.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:51Z",
      "native_id": "10.1038/s42004-026-02209-x",
      "source": "crossref",
      "url": "https://www.nature.com/articles/s42004-026-02209-x"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Structure and Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Representation choice shapes the interpretation of protein conformational dynamics",
  "title_text": "Representation choice shapes the interpretation of protein conformational dynamics",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:51Z",
  "url": "https://research.draconitic.com/paper/9gjq9bjvtnssd",
  "venue": "Communications Chemistry",
  "versions": []
}