The high lethality of the EEEV virus classifies it as an extremely hazardous controlled pathogen. At present, the study of the pathogenic mechanism of the EEEV virus is exceedingly difficult due to the scarcity of valuable biomedical literature. Researchers have determined the structure of EEEV and SFV spike glycoproteins bound to the very low density lipoprotein receptor (VLDLR) ligand binding domain using single-particle cryo-electron microscopy (cryo-EM). The results indicate that EEEV and SFV interact with the same cell receptor through distinct binding modess . This study also employed the bioinformatics domain search method to determine that the EEEV virus P protein adheres to the synaptic membrane via the cholesterol/very low density lipoprotein domain. This shows that we can consistently use the bioinformatics domain search method to explore the biological functions of proteins in high-risk pathogenic viruses like the EEEV virus. Interestingly, this study has made a groundbreaking discovery through the use of this bioinformatics tool. The EEEV virus interferes with synaptic guidance and transmission, causing synaptic depolarization. It then penetrates the synaptic membrane via potassium-like transmembrane nerve channels. Binding to neurotransmitter ligands activates the potassium-like channel function of the EEEV virus, directing the synaptic membrane to produce vesicles that encapsulate the virus and internalize it into the synapse. We anticipate this research to establish a scientific theoretical foundation for the development and design of vaccines and medications.