Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.

Understanding virus antigenicity is of fundamental importance for the development of better, more cross-reactive vaccines. However, as far as we are aware, no systematic work has yet been conducted using the 3D structure of a virus to identify novel epitopes. Therefore we have extended several exist...

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Autores principales:	Daryl W Borley, Mana Mahapatra, David J Paton, Robert M Esnouf, David I Stuart, Elizabeth E Fry
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6b83471f69464865b495a412a7d9cbdf
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spelling	oai:doaj.org-article:6b83471f69464865b495a412a7d9cbdf2021-11-18T07:46:45ZEvaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.1932-620310.1371/journal.pone.0061122https://doaj.org/article/6b83471f69464865b495a412a7d9cbdf2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23667434/?tool=EBIhttps://doaj.org/toc/1932-6203Understanding virus antigenicity is of fundamental importance for the development of better, more cross-reactive vaccines. However, as far as we are aware, no systematic work has yet been conducted using the 3D structure of a virus to identify novel epitopes. Therefore we have extended several existing structural prediction algorithms to build a method for identifying epitopes on the appropriate outer surface of intact virus capsids (which are structurally different from globular proteins in both shape and arrangement of multiple repeated elements) and applied it here as a proof of principle concept to the capsid of foot-and-mouth disease virus (FMDV). We have analysed how reliably several freely available structure-based B cell epitope prediction programs can identify already known viral epitopes of FMDV in the context of the viral capsid. To do this we constructed a simple objective metric to measure the sensitivity and discrimination of such algorithms. After optimising the parameters for five methods using an independent training set we used this measure to evaluate the methods. Individually any one algorithm performed rather poorly (three performing better than the other two) suggesting that there may be value in developing virus-specific software. Taking a very conservative approach requiring a consensus between all three top methods predicts a number of previously described antigenic residues as potential epitopes on more than one serotype of FMDV, consistent with experimental results. The consensus results identified novel residues as potential epitopes on more than one serotype. These include residues 190-192 of VP2 (not previously determined to be antigenic), residues 69-71 and 193-197 of VP3 spanning the pentamer-pentamer interface, and another region incorporating residues 83, 84 and 169-174 of VP1 (all only previously experimentally defined on serotype A). The computer programs needed to create a semi-automated procedure for carrying out this epitope prediction method are presented.Daryl W BorleyMana MahapatraDavid J PatonRobert M EsnoufDavid I StuartElizabeth E FryPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e61122 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daryl W Borley Mana Mahapatra David J Paton Robert M Esnouf David I Stuart Elizabeth E Fry Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
description	Understanding virus antigenicity is of fundamental importance for the development of better, more cross-reactive vaccines. However, as far as we are aware, no systematic work has yet been conducted using the 3D structure of a virus to identify novel epitopes. Therefore we have extended several existing structural prediction algorithms to build a method for identifying epitopes on the appropriate outer surface of intact virus capsids (which are structurally different from globular proteins in both shape and arrangement of multiple repeated elements) and applied it here as a proof of principle concept to the capsid of foot-and-mouth disease virus (FMDV). We have analysed how reliably several freely available structure-based B cell epitope prediction programs can identify already known viral epitopes of FMDV in the context of the viral capsid. To do this we constructed a simple objective metric to measure the sensitivity and discrimination of such algorithms. After optimising the parameters for five methods using an independent training set we used this measure to evaluate the methods. Individually any one algorithm performed rather poorly (three performing better than the other two) suggesting that there may be value in developing virus-specific software. Taking a very conservative approach requiring a consensus between all three top methods predicts a number of previously described antigenic residues as potential epitopes on more than one serotype of FMDV, consistent with experimental results. The consensus results identified novel residues as potential epitopes on more than one serotype. These include residues 190-192 of VP2 (not previously determined to be antigenic), residues 69-71 and 193-197 of VP3 spanning the pentamer-pentamer interface, and another region incorporating residues 83, 84 and 169-174 of VP1 (all only previously experimentally defined on serotype A). The computer programs needed to create a semi-automated procedure for carrying out this epitope prediction method are presented.
format	article
author	Daryl W Borley Mana Mahapatra David J Paton Robert M Esnouf David I Stuart Elizabeth E Fry
author_facet	Daryl W Borley Mana Mahapatra David J Paton Robert M Esnouf David I Stuart Elizabeth E Fry
author_sort	Daryl W Borley
title	Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
title_short	Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
title_full	Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
title_fullStr	Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
title_full_unstemmed	Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
title_sort	evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/6b83471f69464865b495a412a7d9cbdf
work_keys_str_mv	AT darylwborley evaluationanduseofinsilicostructurebasedepitopepredictionwithfootandmouthdiseasevirus AT manamahapatra evaluationanduseofinsilicostructurebasedepitopepredictionwithfootandmouthdiseasevirus AT davidjpaton evaluationanduseofinsilicostructurebasedepitopepredictionwithfootandmouthdiseasevirus AT robertmesnouf evaluationanduseofinsilicostructurebasedepitopepredictionwithfootandmouthdiseasevirus AT davidistuart evaluationanduseofinsilicostructurebasedepitopepredictionwithfootandmouthdiseasevirus AT elizabethefry evaluationanduseofinsilicostructurebasedepitopepredictionwithfootandmouthdiseasevirus
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Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus.

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