CEP: a conformational epitope prediction server

Abstract

CEP server (http://bioinfo.ernet.in/cep.htm) provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag-Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens.

Figure 1

The CEP server home.

Figure 2

A snapshot of predicted AD, CE and graphical display of CE5, which corresponds to the binding site characterized by 1FDL, the complex of lysozyme with Fab D1.3. Note: The amino acid residues with percentage accessibility less than or equal to cut-off are shown in the lower case.