Validation Tools for Predicted Linear B-Epitopes: Antigenicity

Abstract

A important step in designing peptide vaccines involves the identification of antigenic regions in a protein. It will be helpful to synthesize peptides which may elicit antibodies reactive with the intact protein. Earliest method used by Levitt (1976) was folding simulations, other pioneer works by Hopp and Woods (1981), Parker et. al. (1986) are based on the assumption that antigenic regions are primarily hydrophilic regions at the surface of the protein molecule. On the other hand the method presented by Welling, et. al., (1985) is based on the comparison of propensities of amino acids in known antigenic regions in 20 proteins, with that of 314 proteins. While Kolaskar, and Tongaonkar (1990) experimentally observed that if hydrophobic residues occur on the surface of a protein, they are more likely a part of the antigenic sites. In this article, the same method of Welling, et. al. is applied with relatively huge data of 80,592 non redundant proteins of PDB Database, and 344,121 linear b-epitopes of iadb database. The success of antigenicity scale obtained is compared by other five scales on five antigens with known linear b-epitopes.