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A Brief Explanation of Epitope Mapping

A Brief Explanation of Epitope Mapping

Epitope mapping is a process most commonly used in medicine and pharmaceuticals. Scientists can utilize this process, which identifies the binding sites of antibodies and antigens, to identify new diagnoses and develop new vaccines and therapeutics. This brief explanation of epitope mapping will give you a better understanding of the important role epitopes and epitope mapping plays in the study of autoimmune diseases.

Epitope classifications

Sometimes referred to as an antigenic determinant, an epitope is a binding site between an antigen and an antibody. Typically, epitopes contain about five amino acids and create an antibody binding site on an antigen. Epitopes separate into two main classifications based upon their structure. Linear epitopes, also called sequential epitopes, are less common and form a linear structure of amino acids. Conformational epitopes are far more common and contain a three-dimensional tertiary structure which forms as a result of discontiguous amino acid residues. In humans, researchers commonly find conformational and linear epitopes in proteins and peptides.

Epitope mapping

Epitope mapping refers to the process of locating and characterizing antibody and antigen-binding sites. There are several methods available to conduct epitope mapping, but the most common and efficient option is to utilize peptide microarrays and automated extraction systems. Observing analysts can utilize automated microarray spot printing workstations to increase throughput without sacrificing quality or accuracy. In this method, synthetic peptides print onto a glass slide using the automated workstation. Professionals then introduce purified antibodies into the system and will bind to those peptides which display their specific sequence of interest. The observing researcher will remove unbound antibodies and analyze the epitopes of the remaining antibodies and peptides.


Epitope mapping is particularly useful in medicine and pharmaceuticals. Through epitope mapping, scientists can better identify and analyze the antibody and antigen-binding sites of a specific individual. This provides doctors a clearer insight into a patient’s molecular makeup and allows them to build a more individualized and precise treatment option for that patient. The increased clarity provided by epitope mapping also enables scientists to design more effective medicines and vaccines, which they can use for numerous diseases.