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MHC Class II Binding Prediction—A Little Help from a Friend

Vaccines are the greatest single instrument of prophylaxis against infectious diseases, with immeasurable benefits to human wellbeing. The accurate and reliable prediction of peptide-MHC binding is fundamental to the robust identification of T-cell epitopes and thus the successful design of peptide-...

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Detalles Bibliográficos
Autores principales: Dimitrov, Ivan, Garnev, Panayot, Flower, Darren R., Doytchinova, Irini
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875769/
https://www.ncbi.nlm.nih.gov/pubmed/20508817
http://dx.doi.org/10.1155/2010/705821
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author Dimitrov, Ivan
Garnev, Panayot
Flower, Darren R.
Doytchinova, Irini
author_facet Dimitrov, Ivan
Garnev, Panayot
Flower, Darren R.
Doytchinova, Irini
author_sort Dimitrov, Ivan
collection PubMed
description Vaccines are the greatest single instrument of prophylaxis against infectious diseases, with immeasurable benefits to human wellbeing. The accurate and reliable prediction of peptide-MHC binding is fundamental to the robust identification of T-cell epitopes and thus the successful design of peptide- and protein-based vaccines. The prediction of MHC class II peptide binding has hitherto proved recalcitrant and refractory. Here we illustrate the utility of existing computational tools for in silico prediction of peptides binding to class II MHCs. Most of the methods, tested in the present study, detect more than the half of the true binders in the top 5% of all possible nonamers generated from one protein. This number increases in the top 10% and 15% and then does not change significantly. For the top 15% the identified binders approach 86%. In terms of lab work this means 85% less expenditure on materials, labour and time. We show that while existing caveats are well founded, nonetheless use of computational models of class II binding can still offer viable help to the work of the immunologist and vaccinologist.
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spelling pubmed-28757692010-05-27 MHC Class II Binding Prediction—A Little Help from a Friend Dimitrov, Ivan Garnev, Panayot Flower, Darren R. Doytchinova, Irini J Biomed Biotechnol Research Article Vaccines are the greatest single instrument of prophylaxis against infectious diseases, with immeasurable benefits to human wellbeing. The accurate and reliable prediction of peptide-MHC binding is fundamental to the robust identification of T-cell epitopes and thus the successful design of peptide- and protein-based vaccines. The prediction of MHC class II peptide binding has hitherto proved recalcitrant and refractory. Here we illustrate the utility of existing computational tools for in silico prediction of peptides binding to class II MHCs. Most of the methods, tested in the present study, detect more than the half of the true binders in the top 5% of all possible nonamers generated from one protein. This number increases in the top 10% and 15% and then does not change significantly. For the top 15% the identified binders approach 86%. In terms of lab work this means 85% less expenditure on materials, labour and time. We show that while existing caveats are well founded, nonetheless use of computational models of class II binding can still offer viable help to the work of the immunologist and vaccinologist. Hindawi Publishing Corporation 2010 2010-05-20 /pmc/articles/PMC2875769/ /pubmed/20508817 http://dx.doi.org/10.1155/2010/705821 Text en Copyright © 2010 Ivan Dimitrov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Dimitrov, Ivan
Garnev, Panayot
Flower, Darren R.
Doytchinova, Irini
MHC Class II Binding Prediction—A Little Help from a Friend
title MHC Class II Binding Prediction—A Little Help from a Friend
title_full MHC Class II Binding Prediction—A Little Help from a Friend
title_fullStr MHC Class II Binding Prediction—A Little Help from a Friend
title_full_unstemmed MHC Class II Binding Prediction—A Little Help from a Friend
title_short MHC Class II Binding Prediction—A Little Help from a Friend
title_sort mhc class ii binding prediction—a little help from a friend
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875769/
https://www.ncbi.nlm.nih.gov/pubmed/20508817
http://dx.doi.org/10.1155/2010/705821
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