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SPADE web service for prediction of allergen IgE epitopes

The specific interaction of allergens with IgE antibodies and the allergen mediated cross-linking of receptor-bound IgE are key events of allergic diseases. The elucidation of the IgE binding sites (the epitopes) on the allergen surface is an important goal of allergy research. Only few allergen-spe...

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Autores principales: Dall’Antonia, Fabio, Keller, Walter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602491/
https://www.ncbi.nlm.nih.gov/pubmed/31066444
http://dx.doi.org/10.1093/nar/gkz331
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author Dall’Antonia, Fabio
Keller, Walter
author_facet Dall’Antonia, Fabio
Keller, Walter
author_sort Dall’Antonia, Fabio
collection PubMed
description The specific interaction of allergens with IgE antibodies and the allergen mediated cross-linking of receptor-bound IgE are key events of allergic diseases. The elucidation of the IgE binding sites (the epitopes) on the allergen surface is an important goal of allergy research. Only few allergen-specific IgE epitopes have been determined experimentally to date. Epitope prediction methods represent a viable alternative to experimental methods and have worked well with linear epitopes. However, as most IgE epitopes are of conformational and/or discontinuous nature sequence based prediction methods have had limited success in these cases. Here, we present the web server of the program SPADE (https://spade.uni-graz.at), which is the server implementation of a previously published program (1). In this approach we utilize the structural homology of cross-reactive allergens combined with the immunological cross-reactivity data for the discrimination of putative IgE-binding sites from non-cross-reactive surface patches. The method, although predictive, does not rely on machine-learning algorithms and does not require training data. The SPADE server features an easy-to-use interface, an automated pipeline consisting of third-party, as well as own, newly developed routines and a comprehensive output page.
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spelling pubmed-66024912019-07-05 SPADE web service for prediction of allergen IgE epitopes Dall’Antonia, Fabio Keller, Walter Nucleic Acids Res Web Server Issue The specific interaction of allergens with IgE antibodies and the allergen mediated cross-linking of receptor-bound IgE are key events of allergic diseases. The elucidation of the IgE binding sites (the epitopes) on the allergen surface is an important goal of allergy research. Only few allergen-specific IgE epitopes have been determined experimentally to date. Epitope prediction methods represent a viable alternative to experimental methods and have worked well with linear epitopes. However, as most IgE epitopes are of conformational and/or discontinuous nature sequence based prediction methods have had limited success in these cases. Here, we present the web server of the program SPADE (https://spade.uni-graz.at), which is the server implementation of a previously published program (1). In this approach we utilize the structural homology of cross-reactive allergens combined with the immunological cross-reactivity data for the discrimination of putative IgE-binding sites from non-cross-reactive surface patches. The method, although predictive, does not rely on machine-learning algorithms and does not require training data. The SPADE server features an easy-to-use interface, an automated pipeline consisting of third-party, as well as own, newly developed routines and a comprehensive output page. Oxford University Press 2019-07-02 2019-05-08 /pmc/articles/PMC6602491/ /pubmed/31066444 http://dx.doi.org/10.1093/nar/gkz331 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Dall’Antonia, Fabio
Keller, Walter
SPADE web service for prediction of allergen IgE epitopes
title SPADE web service for prediction of allergen IgE epitopes
title_full SPADE web service for prediction of allergen IgE epitopes
title_fullStr SPADE web service for prediction of allergen IgE epitopes
title_full_unstemmed SPADE web service for prediction of allergen IgE epitopes
title_short SPADE web service for prediction of allergen IgE epitopes
title_sort spade web service for prediction of allergen ige epitopes
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602491/
https://www.ncbi.nlm.nih.gov/pubmed/31066444
http://dx.doi.org/10.1093/nar/gkz331
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