{
  "abstract": "Predicting the structural consequences of single-site mutations is fundamental to understanding protein function, disease mechanisms, and protein engineering. However, existing benchmarks for mutation-induced structural change prediction are often affected by duplicate mutation events, highly similar structural pairs, and experimental-state confounders, which can inflate reported performance. We introduce MutaStruct, a curated benchmark of experimentally observed single-mutation protein structure pairs designed for rigorous evaluation of mutation-induced structural changes. MutaStruct combines residue-level sequence validation, coordinate-level quality control, context-aware filtering, event-level deduplication, and leakage-aware data splitting to improve dataset reliability and evaluation rigor. We benchmark sequence-only structure prediction, physics-based refinement, and learning-based refinement methods together with a Copy-WT diagnostic control. Copy-WT remains highly competitive on backbone-based metrics, while method rankings change substantially across local and mutation-site measures. These results show that overall structural fidelity does not necessarily imply accurate modeling of mutation-associated structural change, underscoring the need for further methodological development beyond current paradigms. The benchmark dataset is currently undergoing further curation and expansion and will be released in a future journal-version update. The codebase, trained models, and evaluation pipeline are publicly available at https://github.com/HySonLab/MutaStruct",
  "abstract_shown": true,
  "affiliations": [
    "The University of Alabama at Birmingham, Alabama, United States"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "name": "T.-P. Huynh"
    },
    {
      "name": "D.-M. Ho"
    },
    {
      "name": "V. T. D. Nguyen"
    },
    {
      "name": "Q.-H. Kha"
    },
    {
      "name": "N.-T. Pham"
    },
    {
      "name": "K.-H. Lai"
    },
    {
      "affs": [
        0
      ],
      "name": "T.-S. Hy"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/14rjs7bhgefk8.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.21.760837",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760837v1.full",
  "id": "14rjs7bhgefk8",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760837v1",
  "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",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7223255230",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760837v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/14rjs7bhgefk8.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:12Z",
      "native_id": "10.64898/2026.10.21.760837",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760837v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "MutaStruct: Revisiting Benchmarks for Single-Site Mutation-Induced Structural Change Prediction",
  "title_text": "MutaStruct: Revisiting Benchmarks for Single-Site Mutation-Induced Structural Change Prediction",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:12Z",
  "url": "https://research.draconitic.com/paper/14rjs7bhgefk8",
  "venue": "bioRxiv",
  "versions": []
}