ElliPro is a web-based tool designed to predict antibody epitopes in protein antigens. It implements a method developed by Thornton and colleagues, which identifies continuous epitopes in protein regions protruding from the globular surface. ElliPro combines this method with a residue clustering algorithm, the MODELLER program, and the Jmol viewer to predict and visualize antibody epitopes. The tool was tested on a benchmark dataset of discontinuous epitopes inferred from 3D structures of antibody-protein complexes. Compared to six other structure-based methods, ElliPro performed the best, achieving an AUC value of 0.732 when the most significant prediction was considered for each protein. The tool is available at http://tools.immuneepitope.org/tools/ElliPro. The study suggests that further research on antibody epitopes, incorporating more discriminatory features, could improve prediction accuracy. Additionally, ElliPro's effectiveness in predicting different types of protein-protein interactions is noted, highlighting its potential beyond antibody epitope prediction.ElliPro is a web-based tool designed to predict antibody epitopes in protein antigens. It implements a method developed by Thornton and colleagues, which identifies continuous epitopes in protein regions protruding from the globular surface. ElliPro combines this method with a residue clustering algorithm, the MODELLER program, and the Jmol viewer to predict and visualize antibody epitopes. The tool was tested on a benchmark dataset of discontinuous epitopes inferred from 3D structures of antibody-protein complexes. Compared to six other structure-based methods, ElliPro performed the best, achieving an AUC value of 0.732 when the most significant prediction was considered for each protein. The tool is available at http://tools.immuneepitope.org/tools/ElliPro. The study suggests that further research on antibody epitopes, incorporating more discriminatory features, could improve prediction accuracy. Additionally, ElliPro's effectiveness in predicting different types of protein-protein interactions is noted, highlighting its potential beyond antibody epitope prediction.