Ellipro is a web tool to predicts linear and discontinuous antibody epitopes based on a protein antigen's 3D structure.
Ellipro associates each predicted epitope with a score, defined as a PI (Protrusion Index) value averaged over epitope residues. In this method, the protein's 3D shape is approximated by a number of ellipsoids.
Ellipro implements Thornton's method and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure.
In the test, ellipro gave an AUC value of 0.732, when the most significant prediction was considered for each protein, better than six other structure-based methods.

To use ellipro and get more information, please click here.

Citation:

Ponomarenko JV, Bui H, Li W, Fusseder N, Bourne PE, Sette A, Peters B. 2008. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9:514.PMID: 19055730