title: Prediction of Antigenic B and T Cell Epitopes via Energy Decomposition Analysis: Description of the Web-Based Prediction Tool BEPPE.
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.
authors.affiliation: Department of Computational Biology, Institute for Molecular Recognition Chemistry (ICRM), Italian National Research Council, Milan, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Peri
authors.affiliation: Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
authors.forename: Oscar C
authors.initials: OC
authors.lastname: Solé
authors.affiliation: Institute for Molecular Recognition Chemistry (ICRM), Italian National Research Council, Milan, Italy.|Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy.
authors.forename: Dario
authors.initials: D
authors.lastname: Corrada
authors.affiliation: Department of Computational Biology, Institute for Molecular Recognition Chemistry (ICRM), Italian National Research Council, Milan, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Gori
authors.affiliation: Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.|Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Daura
authors.affiliation: Department of Computational Biology, Institute for Molecular Recognition Chemistry (ICRM), Italian National Research Council, Milan, Italy. giorgio.colombo@icrm.cnr.it.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Colombo
mesh_terms: D000906:Antibodies / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D018604:Epitope Mapping / Q000379:methods; D018985:Epitopes, B-Lymphocyte / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D011485:Protein Binding; D021281:Quantitative Structure-Activity Relationship; D012984:Software; D064878:Web Browser
chemical_list: D000906:Antibodies; D018985:Epitopes, B-Lymphocyte; D018984:Epitopes, T-Lymphocyte
keywords: Antigen–antibody recognition; BEPPE; Energy decomposition; Epitope prediction; MHC-II; PPV; Web server