Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins

Autores
Cossio Pérez, Rodrigo; Palma, Juliana Isabel; Pierdominici Sottile, Gustavo
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
Fil: Cossio Pérez, Rodrigo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Palma, Juliana Isabel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pierdominici Sottile, Gustavo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
Principal component analysis
Molecular dynamics
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:11336/72866
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/72866
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Consistent Principal Component Modes from Molecular Dynamics Simulations of ProteinsCossio Pérez, RodrigoPalma, Juliana IsabelPierdominici Sottile, GustavoPrincipal component analysisMolecular dynamicshttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.Fil: Cossio Pérez, Rodrigo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Palma, Juliana Isabel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pierdominici Sottile, Gustavo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaAmerican Chemical Society2017-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/72866Cossio Pérez, Rodrigo; Palma, Juliana Isabel; Pierdominici Sottile, Gustavo; Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins; American Chemical Society; Journal of Chemical Information and Modeling; 57; 4; 4-2017; 826-8341549-9596CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jcim.6b00646info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jcim.6b00646info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:11:48Zoai:ri.conicet.gov.ar:11336/72866instacron: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 10:11:48.498CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
title Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
spellingShingle Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
Cossio Pérez, Rodrigo
Principal component analysis
Molecular dynamics
title_short Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
title_full Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
title_fullStr Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
title_full_unstemmed Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
title_sort Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins
dc.creator.none.fl_str_mv Cossio Pérez, Rodrigo
Palma, Juliana Isabel
Pierdominici Sottile, Gustavo
author Cossio Pérez, Rodrigo
author_facet Cossio Pérez, Rodrigo
Palma, Juliana Isabel
Pierdominici Sottile, Gustavo
author_role author
author2 Palma, Juliana Isabel
Pierdominici Sottile, Gustavo
author2_role author
author
dc.subject.none.fl_str_mv Principal component analysis
Molecular dynamics
topic Principal component analysis
Molecular dynamics
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
Fil: Cossio Pérez, Rodrigo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Palma, Juliana Isabel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pierdominici Sottile, Gustavo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
publishDate 2017
dc.date.none.fl_str_mv 2017-04
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/11336/72866
Cossio Pérez, Rodrigo; Palma, Juliana Isabel; Pierdominici Sottile, Gustavo; Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins; American Chemical Society; Journal of Chemical Information and Modeling; 57; 4; 4-2017; 826-834
1549-9596
CONICET Digital
CONICET
url http://hdl.handle.net/11336/72866
identifier_str_mv Cossio Pérez, Rodrigo; Palma, Juliana Isabel; Pierdominici Sottile, Gustavo; Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins; American Chemical Society; Journal of Chemical Information and Modeling; 57; 4; 4-2017; 826-834
1549-9596
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jcim.6b00646
info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jcim.6b00646
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
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
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_ 1842270171026161664
score 13.13397

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