A review article that explains how to predict HLA class II binding peptides and candidate epitopes using IEDB tools. The paper discusses the basic features of different prediction methods, the evaluation of their prediction quality and general guidelines for practical use of these tools including evaluation of immunogenicity of protein drugs. The use, advantages and limitations of the methodology are demonstrated taking two previous studies that investigates the immunogenicity of erythropoietin and timothy grass pollen as examples.
Paul, S., Kolla, R.V., Sidney, J., Weiskopf, D., Fleri, W., Kim, Y, Peters, B. and Sette, A. 2013. Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the Immune Epitope Database and Analysis Resource. Clinical and Developmental Immunology.