PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
- Autores
- Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto
- Año de publicación
- 2015
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.
Fil: Emperador, Agustí. Institute for Research in Biomedicine; España
Fil: Sfriso, Pedro. Institute for Research in Biomedicine; España
Fil: Villarreal, Marcos Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Gelpí, Josep Lluis. Institute for Research in Biomedicine; España
Fil: Orozco, Modesto. Institute for Research in Biomedicine; España - Materia
-
Molecular dynamics Simulation
Protein Interaction
Discrete molecular dynamics - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/186239
Ver los metadatos del registro completo
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PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein SystemsEmperador, AgustíSfriso, PedroVillarreal, Marcos ArielGelpí, Josep LluisOrozco, ModestoMolecular dynamics SimulationProtein InteractionDiscrete molecular dynamicshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.Fil: Emperador, Agustí. Institute for Research in Biomedicine; EspañaFil: Sfriso, Pedro. Institute for Research in Biomedicine; EspañaFil: Villarreal, Marcos Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Gelpí, Josep Lluis. Institute for Research in Biomedicine; EspañaFil: Orozco, Modesto. Institute for Research in Biomedicine; EspañaAmerican Chemical Society2015-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/186239Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto; PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems; American Chemical Society; Journal of Chemical Theory and Computation; 11; 12; 11-2015; 5929-59381549-9618CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.5b00660info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.5b00660info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:54:38Zoai:ri.conicet.gov.ar:11336/186239instacron: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:34982025-09-29 09:54:38.915CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
title |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
spellingShingle |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems Emperador, Agustí Molecular dynamics Simulation Protein Interaction Discrete molecular dynamics |
title_short |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
title_full |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
title_fullStr |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
title_full_unstemmed |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
title_sort |
PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems |
dc.creator.none.fl_str_mv |
Emperador, Agustí Sfriso, Pedro Villarreal, Marcos Ariel Gelpí, Josep Lluis Orozco, Modesto |
author |
Emperador, Agustí |
author_facet |
Emperador, Agustí Sfriso, Pedro Villarreal, Marcos Ariel Gelpí, Josep Lluis Orozco, Modesto |
author_role |
author |
author2 |
Sfriso, Pedro Villarreal, Marcos Ariel Gelpí, Josep Lluis Orozco, Modesto |
author2_role |
author author author author |
dc.subject.none.fl_str_mv |
Molecular dynamics Simulation Protein Interaction Discrete molecular dynamics |
topic |
Molecular dynamics Simulation Protein Interaction Discrete molecular dynamics |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins. Fil: Emperador, Agustí. Institute for Research in Biomedicine; España Fil: Sfriso, Pedro. Institute for Research in Biomedicine; España Fil: Villarreal, Marcos Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina Fil: Gelpí, Josep Lluis. Institute for Research in Biomedicine; España Fil: Orozco, Modesto. Institute for Research in Biomedicine; España |
description |
Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-11 |
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/11336/186239 Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto; PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems; American Chemical Society; Journal of Chemical Theory and Computation; 11; 12; 11-2015; 5929-5938 1549-9618 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/186239 |
identifier_str_mv |
Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto; PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems; American Chemical Society; Journal of Chemical Theory and Computation; 11; 12; 11-2015; 5929-5938 1549-9618 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.5b00660 info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.5b00660 |
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 |
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1844613657949896704 |
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13.070432 |