{
  "abstract": "Peptide offers a powerful modality for targeting protein-protein interfaces, yet their computational design remains challenging because sequence identity, backbone geometry and side-chain packing must be optimized simultaneously within a three-dimensional pocket constrained environment. Here we present PeTFlow, a pocket-conditioned all-atom peptide co-design framework that rationalizes this constrained design problem through discrete side-chain state tokenization. In PeTFlow, each residue is represented as a chemically compatible state token, enabling unified modeling of peptide sequence, conformation and all-atom interface geometry. PeTFlow achieved superior generation quality on peptide-design benchmarks and can further be applied to therapeutically relevant peptide drug design.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Phar"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "Q. Deng"
    },
    {
      "name": "M. Xu"
    },
    {
      "name": "H. Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "J. Lei"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f1xjv66ft0awg.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.09.757799",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.09.757799v1.full",
  "id": "f1xjv66ft0awg",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.09.757799v1",
  "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",
      "biochemistry"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7221449544",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.09.757799v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-09",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/f1xjv66ft0awg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:27:11Z",
      "native_id": "10.64898/2026.10.09.757799",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.09.757799v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Structure and Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "PeTFlow: Flow-Matching Based All-Atom Peptide Design through Side-Chain State Tokenization",
  "title_text": "PeTFlow: Flow-Matching Based All-Atom Peptide Design through Side-Chain State Tokenization",
  "type": "preprint",
  "updated_at": "2026-10-30T12:27:11Z",
  "url": "https://research.draconitic.com/paper/f1xjv66ft0awg",
  "venue": "bioRxiv",
  "versions": []
}