Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

Autores
Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; Nielsen, Morten
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4+ T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1.
Fil: Andreatta, Massimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); Argentina
Fil: Karosiene, Edita. La Jolla Institute for Allergy and Immunology; Estados Unidos
Fil: Rasmussen, Michael. Universidad de Copenhagen; Dinamarca
Fil: Stryhn, Anette. Universidad de Copenhagen; Dinamarca
Fil: Buus, Søren. Universidad de Copenhagen; Dinamarca
Fil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); Argentina. Technical University of Denmark; Dinamarca
Materia
Artificial Neural Networks
Binding Core
Mhc Class Ii
Peptide Binding
Peptide-Mhc
T Cell Cross-Reactivity
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/49500
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/49500
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identificationAndreatta, MassimoKarosiene, EditaRasmussen, MichaelStryhn, AnetteBuus, SørenNielsen, MortenArtificial Neural NetworksBinding CoreMhc Class IiPeptide BindingPeptide-MhcT Cell Cross-Reactivityhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4+ T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1.Fil: Andreatta, Massimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); ArgentinaFil: Karosiene, Edita. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Rasmussen, Michael. Universidad de Copenhagen; DinamarcaFil: Stryhn, Anette. Universidad de Copenhagen; DinamarcaFil: Buus, Søren. Universidad de Copenhagen; DinamarcaFil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); Argentina. Technical University of Denmark; DinamarcaSpringer2015-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/49500Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; et al.; Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification; Springer; Immunogenetics; 67; 11-12; 9-2015; 641-6500093-7711CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s00251-015-0873-yinfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs00251-015-0873-yinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:08:14Zoai:ri.conicet.gov.ar:11336/49500instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:08:15.008CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
title Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
spellingShingle Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
Andreatta, Massimo
Artificial Neural Networks
Binding Core
Mhc Class Ii
Peptide Binding
Peptide-Mhc
T Cell Cross-Reactivity
title_short Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
title_full Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
title_fullStr Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
title_full_unstemmed Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
title_sort Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
dc.creator.none.fl_str_mv Andreatta, Massimo
Karosiene, Edita
Rasmussen, Michael
Stryhn, Anette
Buus, Søren
Nielsen, Morten
author Andreatta, Massimo
author_facet Andreatta, Massimo
Karosiene, Edita
Rasmussen, Michael
Stryhn, Anette
Buus, Søren
Nielsen, Morten
author_role author
author2 Karosiene, Edita
Rasmussen, Michael
Stryhn, Anette
Buus, Søren
Nielsen, Morten
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Artificial Neural Networks
Binding Core
Mhc Class Ii
Peptide Binding
Peptide-Mhc
T Cell Cross-Reactivity
topic Artificial Neural Networks
Binding Core
Mhc Class Ii
Peptide Binding
Peptide-Mhc
T Cell Cross-Reactivity
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4+ T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1.
Fil: Andreatta, Massimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); Argentina
Fil: Karosiene, Edita. La Jolla Institute for Allergy and Immunology; Estados Unidos
Fil: Rasmussen, Michael. Universidad de Copenhagen; Dinamarca
Fil: Stryhn, Anette. Universidad de Copenhagen; Dinamarca
Fil: Buus, Søren. Universidad de Copenhagen; Dinamarca
Fil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); Argentina. Technical University of Denmark; Dinamarca
description A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4+ T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1.
publishDate 2015
dc.date.none.fl_str_mv 2015-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/49500
Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; et al.; Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification; Springer; Immunogenetics; 67; 11-12; 9-2015; 641-650
0093-7711
CONICET Digital
CONICET
url http://hdl.handle.net/11336/49500
identifier_str_mv Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; et al.; Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification; Springer; Immunogenetics; 67; 11-12; 9-2015; 641-650
0093-7711
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1007/s00251-015-0873-y
info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs00251-015-0873-y
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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