Among them, the binding energy of the active ingredients with PTGS2 can reach up to −4.75 kcal/mol, indicating that the active ingredients of ginkgo seeds can treat migraine by down-regulating the protein expression of PTGS2, and then blocking the release of prostaglandins such as PGE2. Through the analysis of the KEGG pathway, it was found that cancer, lipid and atherosclerosis, and PI3K-Akt signaling pathways are the main treatment regimens. This evidence concerns the gene PTGS2 and atherosclerosis.