An epitope is that part of an antigen recognised by the immune system, specifically antibodies, B cells, or T cells.  An epitope is a relatively short sequence of amino acids, and a typical full-length protein contains many different epitopes against which antibodies can bind.  The part of an antibody that binds to the epitope is called a paratope.

The immune system is divided into innate and adaptive categories. Innate immunity involves nonspecific defence mechanisms that act immediately or within hours after the microbial invasion.  Adaptive immunity is only present in vertebrates and is highly specific.  The adaptive immune system recognises and destroys invading pathogens individually and remembers the pathogens, a process mediated by T- and B-cells.  These cells do not identify pathogens as a whole but recognise epitopes within them.  Epitopes, a term which can be used interchangeably with antigenic sites or antigenic determinants, can be classified as B cell epitopes or T cell epitopes based on the types of cellular response they elicit.

Identifying epitopes in antigens allows a better understanding of disease aetiology, immune monitoring, developing diagnosis assays, and the design of epitope-based vaccines.

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