Prediction of Antigenic B and T Cell Epitopes via Energy Decomposition Analysis: Description of the Web-Based Prediction Tool BEPPE

  • Claudio Peri
  • Oscar C. Solé
  • Dario Corrada
  • Alessandro Gori
  • Xavier Daura
  • Giorgio ColomboEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1348)


Unraveling the molecular basis of immune recognition still represents a challenging task for current biological sciences, both in terms of theoretical knowledge and practical implications. Here, we describe the physical-chemistry methods and computational protocols for the prediction of antibody-binding epitopes and MHC-II loaded epitopes, starting from the atomic coordinates of antigenic proteins (PDB file). These concepts are the base of the Web tool BEPPE (Binding Epitope Prediction from Protein Energetics), a free service that returns a list of putative epitope sequences and related blast searches against the Uniprot human complete proteome. BEPPE can be employed for the study of the biophysical processes at the basis of the immune recognition, as well as for immunological purposes such as the rational design of biomarkers and targets for diagnostics, therapeutics, and vaccine discovery.


PPV Antigen–antibody recognition MHC-II Epitope prediction Energy decomposition BEPPE Web server 



All authors contributed equally to this new version of the Web tool BEPPE.

This project was supported by EU’s FP6 (“BacAbs”, ref. LSHB-CT-2006-037325) and the Cariplo Foundation (“GtA”, ref. 2009-3577).


  1. 1.
    Scarabelli G, Morra G, Colombo G (2010) Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J 98:1966–1975PubMedCentralCrossRefPubMedGoogle Scholar
  2. 2.
    Lassaux P, Peri C et al (2012) A Structure-Based Strategy for Epitope Discovery in Burkholderia pseudomallei OppA Antigen. Structure 21:167–175CrossRefPubMedGoogle Scholar
  3. 3.
    Peri C, Gagni P et al (2013) Rational Epitope Design for Protein Targeting. ACS Chem Biol 8:397–404CrossRefPubMedGoogle Scholar
  4. 4.
    Gourlay LJ, Peri C et al (2013) Exploiting the Burkholderia pseudomallei Acute Phase Antigen BPSL2765 for Structure-Based Epitope Discovery/Design in Structural Vaccinology. Chem Biol 20:1147–1156CrossRefPubMedGoogle Scholar
  5. 5.
    Ponomarenko JV, Bourne PE (2007) Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7:64PubMedCentralCrossRefPubMedGoogle Scholar
  6. 6.
    Fawcett T (2006) An introduction to ROC analysis. Pattern Recognitt Lett 27:861–974CrossRefGoogle Scholar
  7. 7.
    Tiana G, Simona F, De Mori GM et al (2004) Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci 13:113–124PubMedCentralCrossRefPubMedGoogle Scholar
  8. 8.
    Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 5:403–410CrossRefGoogle Scholar
  9. 9.
  10. 10.
    Duan Y, Wu C, Chowdhury S et al (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012CrossRefPubMedGoogle Scholar
  11. 11.
    Lee MC, Duan Y (2004) Distinguish protein decoys by using a scoring function based on a new Amber force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins 55:620–634CrossRefPubMedGoogle Scholar
  12. 12.
    Hawkins GD, Cramer CJ, Truhlar DG (1995) Pairwise solute descreening of solute charges from a dielectric medium. Chem Phys Lett 246:122–129CrossRefGoogle Scholar
  13. 13.
    Hawkins GD, Cramer CJ, Truhlar DG (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 100:19824–19839CrossRefGoogle Scholar
  14. 14.
    Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 55:383–394CrossRefPubMedGoogle Scholar
  15. 15.
    Amela I, Cedano J, Querol E (2007) Pathogen proteins eliciting antibodies do not share epitopes with host proteins: a bioinformatics approach. PLoS One 2(6):e512PubMedCentralCrossRefPubMedGoogle Scholar
  16. 16.
    The UniProt Consortium (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42:191–198CrossRefGoogle Scholar
  17. 17.
  18. 18.
    Genoni A, Morra G, Colombo G (2012) Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions. J Phys Chem B 116:3331–3343CrossRefPubMedGoogle Scholar
  19. 19.
    Corrada D, Morra G, Colombo G (2013) Investigating allostery in molecular recognition: insights from a computational study of multiple antibody-antigen complexes. J Phys Chem B 117(2):535–552CrossRefPubMedGoogle Scholar
  20. 20.
    Corrada D, Colombo G (2013) Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations. J Chem Inf Model 53(11):2937–2950CrossRefPubMedGoogle Scholar
  21. 21.
  22. 22.
    Mattews BW (1975) Comparison of the predicted and observed secondary structure of T4 phage Lysozyme. Biochim Biophys Acta 405:442–451CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Claudio Peri
    • 1
  • Oscar C. Solé
    • 2
  • Dario Corrada
    • 3
    • 4
  • Alessandro Gori
    • 1
  • Xavier Daura
    • 2
    • 5
  • Giorgio Colombo
    • 1
    Email author
  1. 1.Department of Computational BiologyInstitute for Molecular Recognition Chemistry (ICRM), Italian National Research CouncilMilanItaly
  2. 2.Institut de Biotecnologia i de Biomedicina (IBB)Universitat Autònoma de Barcelona (UAB)BarcelonaSpain
  3. 3.Institute for Molecular Recognition Chemistry (ICRM)Italian National Research CouncilMilanItaly
  4. 4.Department of Earth and Environmental SciencesUniversity of Milano-BicoccaMilanItaly
  5. 5.Catalan Institution for Research and Advanced Studies (ICREA)BarcelonaSpain

Personalised recommendations