CKG-TPI: integrating collaborative knowledge graph with sequence interactions for TCR–peptide binding specificity

Accurately identifying interactions between T-cell receptors (TCRs) and peptides is a fundamental challenge in immunology, with significant implications for vaccine design and immunotherapy. While computational methods offer efficient alternatives to labor-intensive experimental screening, achieving robust and accurate TCR–peptide binding prediction remains a challenging task. To address this, we propose collaborative knowledge graph (CKG-TPI), a novel prediction framework based on graph neural networks that integrates both interaction patterns between TCR and peptide sequences and their higher-order biological context through a constructed collaborative knowledge graph. Experimental results on multiple publicly available independent datasets demonstrate that CKG-TPI consistently outperforms state-of-the-art models. Specifically, it achieves a 9.89% improvement in area under the ROC curve compared to the strongest baseline model UnifyImmun, and a 23.93% increase in area under the precision-recall curve over the leading baseline method. Moreover, attention weight visualization and peptide-specific TCR screening validate the model’s effectiveness, underscoring its potential as a powerful tool for immunological research and therapeutic discovery.