MHCXGRAPH: A GRAPH-BASED APPROACH TO DETECTING T CELL RECEPTOR CROSS- REACTIVITY

T cell receptor (TCR) cross-reactivity, whereby a single TCR is able to recognize different peptides presented by major histocompatibility complex (MHC) molecules, is an intrinsic feature of adaptive immunity that allows the T cell repertoire to respond to a broad diversity of antigens. However, this same property represents an important challenge for the development of T cell based therapeutic strategies, where unintended recognition of alternative targets may lead to undesired effects. Here, we present MHCXGraph, a computational method based on graph theory for the structural analysis of peptide-MHC (pMHC) complexes and the identification of conserved and potentially immunologically relevant regions among them. In MHCXGraph, pMHC structures are represented as graphs, enabling their structural features to be directly compared without relying on sequence or structural alignments. The method provides three complementary analysis modes: Multiple, Pairwise, and Screening, together with adjustable parameters that allow users to configure the analysis according to different biological questions. Results are presented through interpretable and interactive visualization interfaces. MHCXGraph was evaluated across diverse case studies, including peptides bound to classical MHC Class I and Class II molecules, unbound HLA alleles, and pMHC complexes containing non-canonical amino acids. Across these applications, the method identified conserved structural regions that could not be fully captured through sequence similarity alone. By combining structural information with graph-based analysis, MHCXGraph provides an alignment-free and computationally efficient approach for investigating similarities among potentially cross-reactive pMHC targets. Overall, MHCXGraph provides a flexible method for the structural investigation of T cell cross-reactivity and can be incorporated into computational pipelines for de novo pMHC engager design and T cell based vaccine development.