{
  "abstract": "Co-folding models accurately predict biomolecular complexes, but how their internal representations support joint structure prediction remains unclear. We analyze the Boltz-1 trunk by decomposing its pair representation into intra-chain and inter-chain blocks and applying ablation, layer-wise representation geometry, and activation patching. Our results show that structural information is distributed across three streams: the single representation carries token-internal atomic detail, the intra-chain pair representation encodes chain-level geometry, and the inter-chain pair representation controls relative molecular arrangement. Across the trunk depth, representations follow a Mix-Compress-Refine trajectory, while linear probes reveal that intra-chain distance content is largely supplied by MSA preconditioning and inter-chain distance content is constructed progressively across Pairformer layers at each recycle. Apo-holo patching further shows that ligand-induced backbone changes are not fully resolved before diffusion; instead, the diffusion module reconciles partially inconsistent intra- and inter-chain constraints. These findings provide a mechanistic view of how co-folding trunks organize structural information and suggest more partition-aware designs for future biomolecular structure prediction models.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, KAIST"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "M. Park"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Kim"
    },
    {
      "name": "S. Moon"
    },
    {
      "affs": [
        0
      ],
      "name": "H. Kim"
    },
    {
      "name": "G. Jeon"
    },
    {
      "affs": [
        0
      ],
      "name": "W. Y. Kim"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2519axabkaa1m.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.06.749739",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749739v1.full",
  "id": "2519axabkaa1m",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749739v1",
  "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": "W7212049089",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749739v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-06",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/2519axabkaa1m.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:28Z",
      "native_id": "10.64898/2026.09.06.749739",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749739v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "How do Co-Folding Models Organize Structural Information?",
  "title_text": "How do Co-Folding Models Organize Structural Information?",
  "type": "preprint",
  "updated_at": "2026-10-30T12:20:28Z",
  "url": "https://research.draconitic.com/paper/2519axabkaa1m",
  "venue": "bioRxiv",
  "versions": []
}