BEPPE (Binding Epitope Prediction from Protein Energetics)

BEPPE (Binding Epitope Prediction from Protein Energetics) predicts potential antibody binding sites (B cell epitopes) and MHC-II epitopes (T helper cell epitopes) from the 3D structure of antigens.
The predicted epitopes may be in the form of linear as well as discontinuous epitopes.

The method bases on the idea that recognition sites may correspond to localized regions on the surface whose residues are not optimally stabilized, so that they can tolerate variation in their structure and conformational state. This allows them to undergo conformational changes, adapting to the interaction with a binding partner (an antibody, a protein...), and at the same time representing favored sites for cleavage upon antigen degradation.
By this means, the analysis of the energetic properties of a single protein structure can lead to the identification of putative binding sites (For an in-depth explanation of the method, click here).

To carry out the prediction:    
- Upload your protein structure in pdb format.
Or your bundle of pdb files as a zip archive.
- Set the softness level.
This parameter defines the areas to be displayed in the results based on the energy ranking. Lower softness values (1,2) correspond to a strict prediction, focusing on the areas with the strongest energetic de-stabilization. Higher values (4,5) extend the prediction to other potentially relevant areas. The default softness is set to 3.
- Select the energy matrix.
The energy matrix is an approximated reconstruction of the non-bonded interactions of your protein on a residue-pair basis. For the purpose of epitope prediction, the use of the "recommended" energy matrix is preferable in the majority of cases. However, the "alternative" option may be useful in the case of large, multi-domain proteins.
- Insert the email address to receive the results.

For publication of results, please cite:
Scarabelli G, Morra G, Colombo G.
Biophys J. 2010 May 19;98(9):1966-75.
Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping.

Contact adress:

Upload a pdb file or a zip
containing several pdbs
Select the prediction softness level :
Energy matrix :
Insert email adress:

This project is supported by funding under the Sixth Research Framework Programme of the European Union (ref. LSHB-CT-2006-037325)