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3 results on '"BEPPE"'

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

Author

Giorgio Colombo, Dario Corrada, Claudio Peri, Xavier Daura, Oscar Conchillo Solé, Alessandro Gori, Gunnar, H, Peri, C, Solé, O, Corrada, D, Gori, A, Daura, X, and Colombo, G

Subjects
Protein Data Bank (RCSB PDB), Rational design, BEPPE, PPV, Biology, Decomposition analysis, Epitope, World Wide Web, T-Cell Epitopes, Antigen, Epitope prediction, PPV Antigen-antibody recognition MHC-II Epitope prediction Energy decomposition BEPPE Web server, Web server, Proteome, Antigen-antibody recognition, UniProt, Energy decomposition, MHC-II
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.

Published
2015

2. Prediction of antigenic B and T cell epitopes via energy decomposition analysis: Description of the web-based prediction tool BEPPE

Author

Gunnar, H, Peri, C, Solé, O, Corrada, D, Gori, A, Daura, X, Colombo, G, CORRADA, DARIO, Colombo, G., Gunnar, H, Peri, C, Solé, O, Corrada, D, Gori, A, Daura, X, Colombo, G, CORRADA, DARIO, and Colombo, G.

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.

Published
2015

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

Author

Peri C, Solé OC, Corrada D, Gori A, Daura X, and Colombo G

Subjects
Antibodies chemistry, Antibodies immunology, Antibodies metabolism, Computational Biology methods, Epitope Mapping methods, Epitopes, B-Lymphocyte immunology, Epitopes, B-Lymphocyte metabolism, Epitopes, T-Lymphocyte immunology, Epitopes, T-Lymphocyte metabolism, Humans, Protein Binding, Software, Web Browser, Epitopes, B-Lymphocyte chemistry, Epitopes, T-Lymphocyte chemistry, Models, Molecular, Quantitative Structure-Activity Relationship
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.

Published
2015
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