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PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides

Epitope mapping from affinity-selected peptides has become popular in epitope prediction, and correspondingly many Web-based tools have been developed in recent years. However, the performance of these tools varies in different circumstances. To address this problem, we employed an ensemble approach...

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Detalles Bibliográficos
Autores principales: Chen, Wenhan, Guo, William W., Huang, Yanxin, Ma, Zhiqiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360666/
https://www.ncbi.nlm.nih.gov/pubmed/22701536
http://dx.doi.org/10.1371/journal.pone.0037869
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author Chen, Wenhan
Guo, William W.
Huang, Yanxin
Ma, Zhiqiang
author_facet Chen, Wenhan
Guo, William W.
Huang, Yanxin
Ma, Zhiqiang
author_sort Chen, Wenhan
collection PubMed
description Epitope mapping from affinity-selected peptides has become popular in epitope prediction, and correspondingly many Web-based tools have been developed in recent years. However, the performance of these tools varies in different circumstances. To address this problem, we employed an ensemble approach to incorporate two popular Web tools, MimoPro and Pep-3D-Search, together for taking advantages offered by both methods so as to give users more options for their specific purposes of epitope-peptide mapping. The combined operation of Union finds as many associated peptides as possible from both methods, which increases sensitivity in finding potential epitopic regions on a given antigen surface. The combined operation of Intersection achieves to some extent the mutual verification by the two methods and hence increases the likelihood of locating the genuine epitopic region on a given antigen in relation to the interacting peptides. The Consistency between Intersection and Union is an indirect sufficient condition to assess the likelihood of successful peptide-epitope mapping. On average from 27 tests, the combined operations of PepMapper outperformed either MimoPro or Pep-3D-Search alone. Therefore, PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides. The Web server can be freely accessed at: http://informatics.nenu.edu.cn/PepMapper/
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spelling pubmed-33606662012-06-14 PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides Chen, Wenhan Guo, William W. Huang, Yanxin Ma, Zhiqiang PLoS One Research Article Epitope mapping from affinity-selected peptides has become popular in epitope prediction, and correspondingly many Web-based tools have been developed in recent years. However, the performance of these tools varies in different circumstances. To address this problem, we employed an ensemble approach to incorporate two popular Web tools, MimoPro and Pep-3D-Search, together for taking advantages offered by both methods so as to give users more options for their specific purposes of epitope-peptide mapping. The combined operation of Union finds as many associated peptides as possible from both methods, which increases sensitivity in finding potential epitopic regions on a given antigen surface. The combined operation of Intersection achieves to some extent the mutual verification by the two methods and hence increases the likelihood of locating the genuine epitopic region on a given antigen in relation to the interacting peptides. The Consistency between Intersection and Union is an indirect sufficient condition to assess the likelihood of successful peptide-epitope mapping. On average from 27 tests, the combined operations of PepMapper outperformed either MimoPro or Pep-3D-Search alone. Therefore, PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides. The Web server can be freely accessed at: http://informatics.nenu.edu.cn/PepMapper/ Public Library of Science 2012-05-25 /pmc/articles/PMC3360666/ /pubmed/22701536 http://dx.doi.org/10.1371/journal.pone.0037869 Text en Chen et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Chen, Wenhan
Guo, William W.
Huang, Yanxin
Ma, Zhiqiang
PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides
title PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides
title_full PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides
title_fullStr PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides
title_full_unstemmed PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides
title_short PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides
title_sort pepmapper: a collaborative web tool for mapping epitopes from affinity-selected peptides
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360666/
https://www.ncbi.nlm.nih.gov/pubmed/22701536
http://dx.doi.org/10.1371/journal.pone.0037869
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