{
  "abstract": "Biomolecular interactions trigger structural changes of protein complexes essential for cellular signaling, regulation, and drug action. Modern co-folding models can now generate detailed structures of multi-component complexes directly from sequence. However, recent evaluations reveal that they frequently fail to capture specific conformational states induced by a ligand or partner. Here, we show that explicitly modeling the structural transition from an unbound to a bound state, rather than generating the bound complex alone, better resolves these interaction-induced states. Our generative learning framework, K-Fold, transforms independently predicted unbound component priors into an assembled complex through an ultrafast diffusion bridge, operating entirely without multiple sequence alignments. By eliminating co-evolutionary dependencies, K-Fold accurately recovers non-coevolved interfaces in antibody-antigen and targeted-degrader complexes, as well as ligand-directed regulatory states in GPCRs and kinases. Furthermore, by coupling this diffusion bridge with diverse monomeric equilibrium ensembles, K-Fold provides a computationally tractable foundation for sampling complex multi-state landscapes without retraining. These results demonstrate that formulating molecular assembly as an explicit structural transition moves structure prediction beyond static geometries toward capturing biomolecular dynamics.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry; Kim Jaechul Graduate School of AI; Department of AX; InnoCORE AI-CRED Institute, KAIST, Republic of Korea; HITS Inc., Seoul, Republic o"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 33,
  "authors": [
    {
      "name": "Y. Bae"
    },
    {
      "name": "J. Baek"
    },
    {
      "name": "E. Choi"
    },
    {
      "name": "J. H. Choi"
    },
    {
      "name": "H. Han"
    },
    {
      "name": "H. Jang"
    },
    {
      "name": "W. Jeon"
    },
    {
      "name": "J. Jo"
    },
    {
      "affs": [
        0
      ],
      "name": "D. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "H. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "J. H. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "J. H. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "T. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "Y. Kim"
    },
    {
      "name": "J. Lee"
    },
    {
      "name": "J. Lee"
    },
    {
      "name": "S. Moon"
    },
    {
      "name": "M. Park"
    },
    {
      "name": "C. Samuel"
    },
    {
      "name": "H. Seo"
    },
    {
      "name": "J. Seo"
    },
    {
      "name": "S. Seo"
    },
    {
      "name": "M. Shin"
    },
    {
      "name": "Y. Shin"
    },
    {
      "name": "W. Zhung"
    },
    {
      "name": "S. Ahn"
    },
    {
      "name": "D. Han"
    },
    {
      "name": "S. J. Hwang"
    },
    {
      "affs": [
        0
      ],
      "name": "H. M. Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "W. Y. Kim"
    },
    {
      "name": "G. R. Lee"
    },
    {
      "name": "B.-H. Oh"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/56xeacxchmvmp.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.26.760299",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.26.760299v1.full",
  "id": "56xeacxchmvmp",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.26.760299v1",
  "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",
      "molecular biology"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7224128498",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.26.760299v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-26",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/56xeacxchmvmp.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:30:12Z",
      "native_id": "10.64898/2026.10.26.760299",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.26.760299v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:molecular biology",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Predicting conformational changes induced by biomolecular interactions",
  "title_text": "Predicting conformational changes induced by biomolecular interactions",
  "type": "preprint",
  "updated_at": "2026-10-30T12:30:12Z",
  "url": "https://research.draconitic.com/paper/56xeacxchmvmp",
  "venue": "bioRxiv",
  "versions": []
}