Drost Felix, Chernysheva Anna, Albahah Mahmoud, Kocher Katharina, Schober Kilian, Schubert Benjamin
Computational Health Center, Helmholtz Munich, 85764 Neuherberg, Germany; School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany.
Computational Health Center, Helmholtz Munich, 85764 Neuherberg, Germany.
Cell Genom. 2025 Jun 27:100946. doi: 10.1016/j.xgen.2025.100946.
Understanding the recognition of disease-derived epitopes through T cell receptors (TCRs) has the potential to serve as a stepping stone for the development of efficient immunotherapies and vaccines. While a plethora of sequence-based prediction methods for TCR-epitope binding exists, their pre-trained models have not been comparatively evaluated. To alleviate this shortcoming, we integrated 21 TCR-epitope prediction models into the immune-prediction framework ePytope, offering interoperable interfaces with standard TCR repertoire data formats. We showcase the applicability of ePytope-TCR by evaluating the performance of these publicly available prediction models on two challenging datasets. While novel predictors successfully predicted binding to frequently observed epitopes, all methods failed for less frequently observed epitopes. Further, we detected a strong bias in the prediction scores between different epitope classes. We envision this benchmark to guide researchers in their choice of a predictor and to accelerate the method development by defining standardized evaluation settings.
了解通过T细胞受体(TCR)识别疾病衍生表位有潜力成为开发高效免疫疗法和疫苗的垫脚石。虽然存在大量基于序列的TCR-表位结合预测方法,但它们的预训练模型尚未得到比较评估。为了弥补这一不足,我们将21个TCR-表位预测模型集成到免疫预测框架ePytope中,提供与标准TCR库数据格式的可互操作接口。我们通过在两个具有挑战性的数据集上评估这些公开可用预测模型的性能,展示了ePytope-TCR的适用性。虽然新型预测器成功预测了与常见表位的结合,但所有方法在较少见表位上均失败。此外,我们检测到不同表位类别之间的预测分数存在强烈偏差。我们期望这个基准能够指导研究人员选择预测器,并通过定义标准化评估设置来加速方法开发。
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