{
  "abstract": "The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucination. However, existing approaches are predominantly implemented under a single-target, single-state assumption, limiting their ability to model multi-target or multi-state interactions required for advanced function-oriented protein design. Here, we introduce Chamaileon, which unifies multi-target and multi-state binder design by formulating the problem as cross-context binding landscape modeling. The framework is underpinned by a training paradigm termed In-Context Complex Co-Design (I3CD) for context-aware sequence-structure co-modeling. During inference, we employ Mixture-of-Paths Sampling (MoPS), a scalable strategy that optimizes a single sequence across contexts while alleviating the scarcity of high-quality multi-conformational paired data. Extensive evaluation on our newly constructed benchmark, CROSS, demonstrates that Chamaileon effectively generates sequences adaptable to diverse conformational landscapes and multi-target requirements. The code is available on https://github.com/caohengyuan/Chamaileon.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2607.23518",
  "author_total": 8,
  "authors": [
    {
      "name": "Hengyuan Cao"
    },
    {
      "name": "Shizhuo Cheng"
    },
    {
      "name": "Mingxuan Liu"
    },
    {
      "name": "Weicheng Huang"
    },
    {
      "name": "Yunhong Lu"
    },
    {
      "name": "Chenxi Cai"
    },
    {
      "name": "Yan Zhang"
    },
    {
      "name": "Min Zhang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/exd1kysqknp70.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2607.23518",
  "fulltext_url": null,
  "id": "exd1kysqknp70",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2607.23518",
  "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",
      "q-bio.BM"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7171494357",
  "pdf_url": "https://arxiv.org/pdf/2607.23518",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-13",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/exd1kysqknp70.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:30Z",
      "native_id": "2607.23518",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2607.23518"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "arxiv:q-bio.BM",
      "subfield": "biophysics"
    }
  ],
  "title": "Chamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling",
  "title_text": "Chamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:30Z",
  "url": "https://research.draconitic.com/paper/exd1kysqknp70",
  "venue": "arXiv",
  "versions": []
}