Background: Guillain-Barré Syndrome (GBS) and multiple sclerosis are autoimmune diseases associated with an immune system attack response against peripheral and central nervous system autoantigens, respectively. Given the potential of Epstein-Barr virus (EBV) as a risk factor for both multiple sclerosis and GBS, the present study aimed to identify crucial residues among potential EBV CD4+ T lymphocyte epitopes and nervous system proteins. Methods: Public databases (Allele Frequency Net Database, Immune Epitope Database, Genevestigator, and Protein Atlas) were used to select proteins abundant in the nervous system, EBV immunogenic proteins, and HLA haplotypes. Computational tools were employed for predicting HLA-binding peptides and immunogenicity. For this, we developed immuno-cross, a Python tool (https://github.com/evoMOL-Lab/immuno-cross) to compare residue identity among nonamers. Results: We found ten proteins from the nervous system and 28 from EBV, which were used for predicting the binding peptides of 21 common HLAs in the world population. A total of 1411 haplotypes were distributed among 51 pairs of HLAs. Simulations were performed to determine whether nonamers from the EBV and nervous system proteins targeted TCR-contact residues. Three selection criteria based on the relevance of each contact in the TCR-peptide-MHC interaction. The primary contact should be located at position P5, with positions P2, P3, and P8 considered secondary, and P4, P6, and P7 tertiary. Nonamers of EBV proteins and myelin proteins were combined in pairs and compared based on predefined selection criteria. The Periaxin protein had the highest number of nonamers pairs among PNS proteins, with 35 pairs. Four nonamers pairs from APLP1, two from CNP, and two from MBP bind to alleles of the haplotype DR-15. Conclusion: The new approach proposed here revealed that peptides derived from nervous system and EBV proteins share identical residues at these critical contact points, which supports molecular mimicry. These findings suggest cross-reactivity between them and that the nonamer pairs identified with this approach have the potential to be an autoantigen. Experimental studies are needed to validate these findings.