Bepitope is a computer tool for predicting the antigenic sites of a protein. Odorico M. and Pellequer J.-L. (2003) BEPITOPE : predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recognit. 16 : 20-22. A modern version of the original PREDITOP tool : Pellequer J-L and Westhof E (1993) PREDITOP : a program for antigenicity predictions. J. Mol. Graph. 11 : 204-210.
An antigenic site is the region of a protein that is / will be recognized by an antibody molecule. The goal of Bepitope is to identify the antigenic sites of a protein that will tend to adopt the same cognate 3D structure once synthesized as a peptide.
Experimentally, once the region is identified, the peptide will be synthesized and then injected into the host to produce antibodies. Thanks to the phenomenon of the cross-reaction, the antibody recognizing the peptide will have the possibility of recognizing the parent protein from which the peptide is derived.
This is a big challenge in protein engineering because it is rare that a protein fragment, once synthesized as a peptide, adopts the same local 3D structure as that present in the structure of the entire protein. Nevertheless, it has been shown that peptides in solution often adopt a beta-strand structure.
The idea behind Bepitope’s Pellequer method is therefore to identify the regions in beta turn of a protein thus increasing the chances of cross reactions between an antipeptide antibody and the native parent protein.
The new online version of Bepitope is here >>>>>>>>>>>>> : bepitope.ibs.fr
A tutorial will be provided soon.