Prediction of Antigenic Epitope Patches on Protein Surface Using Antigen Structure Information and Support Vector Machine

Identification of antigen-antibody interacting sites is an important task for vaccine design, and hence reliable computer based prediction methods are highly desirable. The prediction performances of the current existing methods to predict the conformational B-cell epitope residues are still not satisfying and remain far from ideal. This is a new approach in the area of vaccine development to predict the antigenic surface patches that hold the majority number of epitope residues in the surface of the antigen protein structure. The proposed method is a support vector machine based model to predict the epitope patches in the antigen structures by combining the accessible surface area and B-factor structural features. The Predictions are made for the known structures of benchmark dataset after removing antigens sequence redundancy where no two antigen sequences have more than 40% sequence identity. The predictions are successful for 70% of the antigen structure chains of the benchmark dataset. We compared the prediction performance of our model with a protein – protein interaction prediction server “Sharp2” using the same antigen structures of the benchmark dataset and observed that our model outperforms on Sharp2 by more than 40% accuracy. This paper demonstrates that the identification of the antigenic determinant sites in the protein surface using the antigen structural information outperforms the traditional protein-protein interaction algorithms to predict the interacting sites in the antigen protein surface. It provides a new approach for the scientists to only use the predicted antigenic epitope surface patch from the target antigen structure in vaccine development rather than using the predicted epitope residues. A web server “PatchTope” has been developed for predicting antigenic epitope surface patches on an antigen protein structure surface and is available at http://www.fci.cu.edu.eg:8080/PatchTope/.