Epitope Mapping (also called antibody epitope mapping) is the set of experimental and computational approaches used to identify the precise antigen features an antibody recognizes and binds—down to specific amino acids, structural patches, or even interaction “hot spots.” In immunology terms, the epitope is the binding site on the antigen, while the antibody’s complementary binding surface is the paratope. Knowing exactly where binding occurs is foundational for understanding immune recognition, improving biologics, and designing better diagnostics and vaccines. Why Epitope Mapping Matters (Beyond “It Binds”) Antibodies can bind the same antigen in very different ways. Two antibodies may both “hit” the same protein yet differ dramatically in neutralization strength, cross-reactivity, or tolerance to mutations. Epitope mapping turns binding into actionable knowledge, helping teams: Differentiate antibodies that otherwise look similar by affinity alone (e.g., classifying binding regions and overlap patterns). Explain potency and mechanism of action, especially when blocking a receptor site or preventing conformational changes. Reduce off-target risk by detecting binding to conserved motifs shared across proteins. Guide design decisions for vaccines and diagnostics by focusing on minimal, protective, or assay-relevant epitopes. Two Big Epitope Types: Linear vs Conformational A key concept for practical…
