The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels

Autores
Klein, Florencia; Soñora, Martín; Helene Santos, Lucianna; Frigini, Ezequiel Nazareno; Ballesteros-Casallas, Andrés; Rodrigo Machado, Matías; Pantano, Sergio
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows. However, a holistic view of biological ensembles' structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward. This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.
Fil: Klein, Florencia. Laboratoire de Biochimie Théorique; Francia
Fil: Soñora, Martín. Instituto Pasteur de Montevideo; Uruguay
Fil: Helene Santos, Lucianna. Instituto Pasteur de Montevideo; Uruguay
Fil: Frigini, Ezequiel Nazareno. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; Argentina
Fil: Ballesteros-Casallas, Andrés. Instituto Pasteur de Montevideo; Uruguay
Fil: Rodrigo Machado, Matías. Instituto Pasteur de Montevideo; Uruguay
Fil: Pantano, Sergio. Instituto Pasteur de Montevideo; Uruguay
Materia
COARSE-GRAINED
MOLECULAR DYNAMICS
MULTISCALE MODELS
SIMULATIONS
SIRAH
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:11336/227402
Acceder
id CONICETDig_f5b9188368be54e0a8d2aa116ecede6c
oai_identifier_str oai:ri.conicet.gov.ar:11336/227402
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levelsKlein, FlorenciaSoñora, MartínHelene Santos, LuciannaFrigini, Ezequiel NazarenoBallesteros-Casallas, AndrésRodrigo Machado, MatíasPantano, SergioCOARSE-GRAINEDMOLECULAR DYNAMICSMULTISCALE MODELSSIMULATIONSSIRAHhttps://purl.org/becyt/ford/1.7https://purl.org/becyt/ford/1The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows. However, a holistic view of biological ensembles' structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward. This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.Fil: Klein, Florencia. Laboratoire de Biochimie Théorique; FranciaFil: Soñora, Martín. Instituto Pasteur de Montevideo; UruguayFil: Helene Santos, Lucianna. Instituto Pasteur de Montevideo; UruguayFil: Frigini, Ezequiel Nazareno. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Ballesteros-Casallas, Andrés. Instituto Pasteur de Montevideo; UruguayFil: Rodrigo Machado, Matías. Instituto Pasteur de Montevideo; UruguayFil: Pantano, Sergio. Instituto Pasteur de Montevideo; UruguayAcademic Press Inc Elsevier Science2023-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/227402Klein, Florencia; Soñora, Martín; Helene Santos, Lucianna; Frigini, Ezequiel Nazareno; Ballesteros-Casallas, Andrés; et al.; The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels; Academic Press Inc Elsevier Science; Journal Of Structural Biology; 215; 3; 6-2023; 1-311047-8477CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S1047847723000485info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jsb.2023.107985info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:35:32Zoai:ri.conicet.gov.ar:11336/227402instacron: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:34982025-10-15 14:35:33.195CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
title The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
spellingShingle The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
Klein, Florencia
COARSE-GRAINED
MOLECULAR DYNAMICS
MULTISCALE MODELS
SIMULATIONS
SIRAH
title_short The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
title_full The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
title_fullStr The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
title_full_unstemmed The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
title_sort The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
dc.creator.none.fl_str_mv Klein, Florencia
Soñora, Martín
Helene Santos, Lucianna
Frigini, Ezequiel Nazareno
Ballesteros-Casallas, Andrés
Rodrigo Machado, Matías
Pantano, Sergio
author Klein, Florencia
author_facet Klein, Florencia
Soñora, Martín
Helene Santos, Lucianna
Frigini, Ezequiel Nazareno
Ballesteros-Casallas, Andrés
Rodrigo Machado, Matías
Pantano, Sergio
author_role author
author2 Soñora, Martín
Helene Santos, Lucianna
Frigini, Ezequiel Nazareno
Ballesteros-Casallas, Andrés
Rodrigo Machado, Matías
Pantano, Sergio
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv COARSE-GRAINED
MOLECULAR DYNAMICS
MULTISCALE MODELS
SIMULATIONS
SIRAH
topic COARSE-GRAINED
MOLECULAR DYNAMICS
MULTISCALE MODELS
SIMULATIONS
SIRAH
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.7
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows. However, a holistic view of biological ensembles' structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward. This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.
Fil: Klein, Florencia. Laboratoire de Biochimie Théorique; Francia
Fil: Soñora, Martín. Instituto Pasteur de Montevideo; Uruguay
Fil: Helene Santos, Lucianna. Instituto Pasteur de Montevideo; Uruguay
Fil: Frigini, Ezequiel Nazareno. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; Argentina
Fil: Ballesteros-Casallas, Andrés. Instituto Pasteur de Montevideo; Uruguay
Fil: Rodrigo Machado, Matías. Instituto Pasteur de Montevideo; Uruguay
Fil: Pantano, Sergio. Instituto Pasteur de Montevideo; Uruguay
description The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows. However, a holistic view of biological ensembles' structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward. This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.
publishDate 2023
dc.date.none.fl_str_mv 2023-06
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/11336/227402
Klein, Florencia; Soñora, Martín; Helene Santos, Lucianna; Frigini, Ezequiel Nazareno; Ballesteros-Casallas, Andrés; et al.; The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels; Academic Press Inc Elsevier Science; Journal Of Structural Biology; 215; 3; 6-2023; 1-31
1047-8477
CONICET Digital
CONICET
url http://hdl.handle.net/11336/227402
identifier_str_mv Klein, Florencia; Soñora, Martín; Helene Santos, Lucianna; Frigini, Ezequiel Nazareno; Ballesteros-Casallas, Andrés; et al.; The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels; Academic Press Inc Elsevier Science; Journal Of Structural Biology; 215; 3; 6-2023; 1-31
1047-8477
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://linkinghub.elsevier.com/retrieve/pii/S1047847723000485
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jsb.2023.107985
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 Academic Press Inc Elsevier Science
publisher.none.fl_str_mv Academic Press Inc Elsevier Science
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_ 1846082815814270976
score 13.22299

Publicaciones similares