An assessment of prediction methods for locating continuous epitopes in proteins

Many attempts have been made to predict the position of antigenic sites in proteins from certain features of their primary structure. Parameters such as the hydrophilicity, static accessibility and mobility of short segments of polypeptide chains have been correlated with the location of continuous epitopes in proteins. Relative scales describing the structural propensity of each of the 20 amino acids have been derived and these are commonly used for constructing structural prediction profiles and for locating the position of epitopes. The predictive value of algorithms based on eight such scales has been compared in the present study, using as antigenicity data base the location of 29 continuous epitopes in four model proteins. A chi 2 statistical analysis showed that a segmental mobility scale and a hydrophilicity scale based on peptide retention times during chromatography gave the highest level of correct predictions.