LYRA, a webserver for lymphocyte receptor structural modeling

Autores
Klausen, Michael Schantz; Anderson, Mads Valdemar; Jespersen, Martin Closter; Nielsen, Morten; Marcatili, Paolo
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for nonspecialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure.
Fil: Klausen, Michael Schantz. Technical University of Denmark; Dinamarca
Fil: Anderson, Mads Valdemar. Technical University of Denmark; Dinamarca
Fil: Jespersen, Martin Closter. Technical University of Denmark; Dinamarca
Fil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Marcatili, Paolo. Technical University of Denmark; Dinamarca
Materia
TCR
BCR
Lymphocyte receptor
Structural modeling
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:11336/49402
Acceder
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network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling LYRA, a webserver for lymphocyte receptor structural modelingKlausen, Michael SchantzAnderson, Mads ValdemarJespersen, Martin ClosterNielsen, MortenMarcatili, PaoloTCRBCRLymphocyte receptorStructural modelinghttps://purl.org/becyt/ford/3.1https://purl.org/becyt/ford/3The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for nonspecialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure.Fil: Klausen, Michael Schantz. Technical University of Denmark; DinamarcaFil: Anderson, Mads Valdemar. Technical University of Denmark; DinamarcaFil: Jespersen, Martin Closter. Technical University of Denmark; DinamarcaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Marcatili, Paolo. Technical University of Denmark; DinamarcaOxford University Press2015-05info: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/11336/49402Klausen, Michael Schantz; Anderson, Mads Valdemar; Jespersen, Martin Closter; Nielsen, Morten; Marcatili, Paolo; LYRA, a webserver for lymphocyte receptor structural modeling; Oxford University Press; Nucleic Acids Research; 43; W1; 5-2015; W349-W3550305-10481362-4962CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkv535info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/nar/article/43/W1/W349/2467978info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489227/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:08:46Zoai:ri.conicet.gov.ar:11336/49402instacron: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 10:08:47.345CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv LYRA, a webserver for lymphocyte receptor structural modeling
title LYRA, a webserver for lymphocyte receptor structural modeling
spellingShingle LYRA, a webserver for lymphocyte receptor structural modeling
Klausen, Michael Schantz
TCR
BCR
Lymphocyte receptor
Structural modeling
title_short LYRA, a webserver for lymphocyte receptor structural modeling
title_full LYRA, a webserver for lymphocyte receptor structural modeling
title_fullStr LYRA, a webserver for lymphocyte receptor structural modeling
title_full_unstemmed LYRA, a webserver for lymphocyte receptor structural modeling
title_sort LYRA, a webserver for lymphocyte receptor structural modeling
dc.creator.none.fl_str_mv Klausen, Michael Schantz
Anderson, Mads Valdemar
Jespersen, Martin Closter
Nielsen, Morten
Marcatili, Paolo
author Klausen, Michael Schantz
author_facet Klausen, Michael Schantz
Anderson, Mads Valdemar
Jespersen, Martin Closter
Nielsen, Morten
Marcatili, Paolo
author_role author
author2 Anderson, Mads Valdemar
Jespersen, Martin Closter
Nielsen, Morten
Marcatili, Paolo
author2_role author
author
author
author
dc.subject.none.fl_str_mv TCR
BCR
Lymphocyte receptor
Structural modeling
topic TCR
BCR
Lymphocyte receptor
Structural modeling
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for nonspecialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure.
Fil: Klausen, Michael Schantz. Technical University of Denmark; Dinamarca
Fil: Anderson, Mads Valdemar. Technical University of Denmark; Dinamarca
Fil: Jespersen, Martin Closter. Technical University of Denmark; Dinamarca
Fil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Marcatili, Paolo. Technical University of Denmark; Dinamarca
description The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for nonspecialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure.
publishDate 2015
dc.date.none.fl_str_mv 2015-05
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/11336/49402
Klausen, Michael Schantz; Anderson, Mads Valdemar; Jespersen, Martin Closter; Nielsen, Morten; Marcatili, Paolo; LYRA, a webserver for lymphocyte receptor structural modeling; Oxford University Press; Nucleic Acids Research; 43; W1; 5-2015; W349-W355
0305-1048
1362-4962
CONICET Digital
CONICET
url http://hdl.handle.net/11336/49402
identifier_str_mv Klausen, Michael Schantz; Anderson, Mads Valdemar; Jespersen, Martin Closter; Nielsen, Morten; Marcatili, Paolo; LYRA, a webserver for lymphocyte receptor structural modeling; Oxford University Press; Nucleic Acids Research; 43; W1; 5-2015; W349-W355
0305-1048
1362-4962
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkv535
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/nar/article/43/W1/W349/2467978
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489227/
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 Oxford University Press
publisher.none.fl_str_mv Oxford University Press
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
_version_ 1842270057360523264
score 13.13397

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