Epitope mapping is the identification of the specific regions of a protein recognized by the antibody binding site. The protein is clipped into fragments, or fragments are expressed recombinantly, and tested for binding by antibody. This narrows down the protein region of antibody binding. A series of synthetic peptides containing overlapping amino acid sequences based on the protein structure are also constructed and the exact epitope recognized by the antibody can be determined by analyzing which peptides are bound by the antibody. This would be a linear determinant epitope. Some epitopes depend on a tertiary conformation structure and antibody binding may only occur with large protein fragments

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