Table 1_NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions.docx

Accurate modeling of T cell receptor (TCR)–peptide–major histocompatibility complex (pMHC) interactions is critical for understanding immune recognition. In this study, we present advances in structural modeling of TCR-pMHC class I complexes focusing on improving docking quality scoring and structural model selection using graph neural networks (GNN). We find that AlphaFold-Multimer’s confidence score in certain cases correlates poorly with DockQ quality scores, leading to overestimation of model accuracy. Our proposed GNN solution achieves a 25% increase in Spearman’s correlation between predicted quality and DockQ (from 0.681 to 0.855) and improves docking candidate ranking. Additionally, the GNN completely avoids selection of failed structures. Additionally, we assess the ability of our models to distinguish binding from non-binding TCR-pMHC interactions based on their predicted quality. Here, we demonstrate that our proposed model, particularly for high-quality structural models, is capable of discriminating between binding and non-binding complexes in a zero-shot setting. However, our findings also underlined that the structural pipeline struggled to generate sufficiently accurate TCR-pMHC models for reliable binding classification, highlighting the need for further improvements in modeling accuracy.