{
  "abstract": "We propose EMBER, a structure-based framework for TCR--pMHC binding prediction that eliminates the need for a predicted docked complex, and with it the placement error that dominates such predictions. Traditional structure-based predictors utilize the co-folded complex structure of the receptor and the antigen and interpret binding from its contact surface. Consequently, every downstream feature inherits any deviation the structure-prediction tool introduced. Methodologically, EMBER folds the TCR and pMHC independently, encodes them as SE(3)-invariant residue graphs, and compares their learned representations without constructing a shared coordinate frame. A relative pose is therefore not an input of the model, so placement error cannot propagate into the prediction. Computationally, EMBER preprocesses $O(N{+}M)$ monomer folds where a complex-based predictor needs $O(NM)$ operations. Experimentally, under epitope-disjoint evaluation with six retrained baselines, EMBER is first on every metric under all four folding tools, by 0.9 to 14.4% in micro-AUROC, 18.5 to 25.3% in micro-AUPRC and 10.6 to 24.1% in MCC. Its ranking is also up to 85% more stable across folding tools.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2610.27334",
  "author_total": 6,
  "authors": [
    {
      "name": "Lin Ha"
    },
    {
      "name": "Chen Zhou"
    },
    {
      "name": "Haozheng Luo"
    },
    {
      "name": "Han Liu"
    },
    {
      "name": "Xiaoyu Zhang"
    },
    {
      "name": "Yan Chen"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9g1pe2dtdp3pa.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2610.27334",
  "fulltext_url": null,
  "id": "9g1pe2dtdp3pa",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2610.27334",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cs.LG"
    ],
    [
      "arxiv",
      "q-bio.QM"
    ],
    [
      "openalex",
      "1312|vaccines and immunoinformatics approaches"
    ]
  ],
  "openalex": "W7223090195",
  "pdf_url": "https://arxiv.org/pdf/2610.27334",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-19",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9g1pe2dtdp3pa.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:34:08Z",
      "native_id": "2610.27334",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2610.27334"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.QM",
      "subfield": "bioinformatics"
    }
  ],
  "title": "EMBER: Predicting TCR--pMHC Binding Without a Docked Complex",
  "title_text": "EMBER: Predicting TCR--pMHC Binding Without a Docked Complex",
  "type": "preprint",
  "updated_at": "2026-10-30T12:34:08Z",
  "url": "https://research.draconitic.com/paper/9g1pe2dtdp3pa",
  "venue": "arXiv",
  "versions": []
}