An epitope is the part of a foreign organism or its proteins that is being recognized by the immune system, specifically by antibodies, B cells, or cytotoxic T cells.
Most epitopes can be thought of as three-dimensional surface features of an antigen molecule; these features fit precisely and thus bind to antibodies. Exceptions are linear epitopes, which are determined by the amino acid sequence (the primary structure) rather than by the tertiary structure of a protein.
Epitopes can be mapped using protein microarrays, and with the ELISPOT or ELISA techniques.
Epitopes that are recognised by common antibodies can be fused to genes, thus aiding further molecular characterization of the gene product. Common epitopes used for this purpose are c-myc, HA, FLAG, V5.