B-CELL EPITOPE PREDICTION
When a living organism encounters a pathogenic virus or microbe, the B cells of the immune system recognize the pathogen’s antigens by their membrane-bound immunoglobulin receptors and, in response, produce antibodies specific to these antigens. The term antigen refers to any entity—a cell, a macromolecular assembly, or a molecule—that may be bound by either a B-cell receptor or an antibody molecule. The binding portion of an antigen is called a B-cell epitope or an antigenic determinant. If an antigen is a protein, an epitope may be either a short peptide from the protein sequence or a patch of atoms on the protein surface in the three-dimensional space. Since other types of epitopes, such as T-cell epitopes, are not discussed in this chapter, B-cell epitopes will be referred to as epitopes.
The property of an antigen to bind specifically complementary antibodies is known as the antigen’s antigenicity; likewise, the ability of an antigen to induce an immune response is called its immunogenicity. Neither antigenicity nor immunogenicity is an intrinsic feature of the antigen. Antigenicity is defined with respect to a specific antibody, and an epitope thus acquires an identity only because an antibody is able to bind to it. The entire accessible surface of an antigen is likely to be recognized by a large panel of antibodies that is large enough (Berzofsky, 1985). Although an antigen’s antigenicity ...