Weighted lambda superstrings applied to vaccine design
dc.contributor.author | Martínez Fernández, Luis ![]() | |
dc.contributor.author | Milanič, Martin | |
dc.contributor.author | Malaina Celada, Iker ![]() | |
dc.contributor.author | Álvarez, Carmen | |
dc.contributor.author | Pérez Pinilla, Martín Blas ![]() | |
dc.contributor.author | Martínez de la Fuente Martínez, Ildefonso Abel | |
dc.date.accessioned | 2019-03-26T13:21:02Z | |
dc.date.available | 2019-03-26T13:21:02Z | |
dc.date.issued | 2019-02-08 | |
dc.identifier.citation | PLOS ONE 14(2) : (2019) // Article ID e0211714 | es_ES |
dc.identifier.issn | 1932-6203 | |
dc.identifier.uri | http://hdl.handle.net/10810/32164 | |
dc.description.abstract | We generalize the notion of lambda-superstrings, presented in a previous paper, to the notion of weighted lambda-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted lambda-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic lambda-superstrings that at the same time present similar conformations to the Nef virus proteins. | es_ES |
dc.description.sponsorship | This research was supported in part by the Basque Government, grants IT753-13 and IT974-16 and by the UPV/EHU and Basque Center of Applied Mathematics, grant US18/21. This research was also in part by the Slovenian Research Agency (I0-0035, research program P1-0285, and research projects N1-0032, J1-7051, and J1-9110). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Public Library Science | es_ES |
dc.rights | info:eu-repo/semantics/openAccess | es_ES |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/es/ | * |
dc.subject | T-cell epitope | es_ES |
dc.subject | immunogenicity | es_ES |
dc.subject | prediction | es_ES |
dc.subject | algorithm | es_ES |
dc.subject | CD4(+) | es_ES |
dc.subject | protein-structure | es_ES |
dc.title | Weighted lambda superstrings applied to vaccine design | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.rights.holder | © 2019 Martínez et al. 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 credited. | es_ES |
dc.rights.holder | Atribución 3.0 España | * |
dc.relation.publisherversion | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211714 | es_ES |
dc.identifier.doi | 10.1371/journal.pone.0211714 | |
dc.departamentoes | Matemáticas | es_ES |
dc.departamentoeu | Matematika | es_ES |
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Except where otherwise noted, this item's license is described as © 2019 Martínez et al. 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 credited.