Peptide Antibodies pp 13-22

Part of the Methods in Molecular Biology book series (MIMB, volume 1348)

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 Colombo

Abstract

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.

Keywords

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

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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
  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

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