MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions

Autores
Li, Minghui; Simonetti, Franco Lucio; Goncearenco, Alexander; Panchenko, Anna R.
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of impacts of variants on proteins. To address this need we introduce a new computational method MutaBind to evaluate the effects of sequence variants and disease mutations on protein interactions and calculate the quantitative changes in binding affinity. The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain optimization algorithms. The MutaBind server maps mutations on a structural protein complex, calculates the associated changes in binding affinity, determines the deleterious effect of a mutation, estimates the confidence of this prediction and produces a mutant structural model for download. MutaBind can be applied to a large number of problems, including determination of potential driver mutations in cancer and other diseases, elucidation of the effects of sequence variants on protein fitness in evolution and protein design. MutaBind is available at http://www.ncbi.nlm.nih.gov/projects/mutabind/.
Fil: Li, Minghui. National Institutes Of Health; Estados Unidos
Fil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina
Fil: Goncearenco, Alexander. National Institutes Of Health; Estados Unidos
Fil: Panchenko, Anna R.. National Institutes Of Health; Estados Unidos
Materia
PROTEIN PROTEIN INTERACTION
MUTATION
SEQUENCE VARIANTS
SERVER
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:11336/18159
Acceder
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network_name_str CONICET Digital (CONICET)
spelling MutaBind estimates and interprets the effects of sequence variants on protein-protein interactionsLi, MinghuiSimonetti, Franco LucioGoncearenco, AlexanderPanchenko, Anna R.PROTEIN PROTEIN INTERACTIONMUTATIONSEQUENCE VARIANTSSERVERhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of impacts of variants on proteins. To address this need we introduce a new computational method MutaBind to evaluate the effects of sequence variants and disease mutations on protein interactions and calculate the quantitative changes in binding affinity. The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain optimization algorithms. The MutaBind server maps mutations on a structural protein complex, calculates the associated changes in binding affinity, determines the deleterious effect of a mutation, estimates the confidence of this prediction and produces a mutant structural model for download. MutaBind can be applied to a large number of problems, including determination of potential driver mutations in cancer and other diseases, elucidation of the effects of sequence variants on protein fitness in evolution and protein design. MutaBind is available at http://www.ncbi.nlm.nih.gov/projects/mutabind/.Fil: Li, Minghui. National Institutes Of Health; Estados UnidosFil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Goncearenco, Alexander. National Institutes Of Health; Estados UnidosFil: Panchenko, Anna R.. National Institutes Of Health; Estados UnidosOxford University Press2016-05info: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/11336/18159Li, Minghui; Simonetti, Franco Lucio; Goncearenco, Alexander; Panchenko, Anna R.; MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions; Oxford University Press; Nucleic Acids Research; 44; W1; 5-2016; W494-5010305-10481362-4962CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw374info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkw374info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:18:25Zoai:ri.conicet.gov.ar:11336/18159instacron: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 10:18:25.769CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
title MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
spellingShingle MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
Li, Minghui
PROTEIN PROTEIN INTERACTION
MUTATION
SEQUENCE VARIANTS
SERVER
title_short MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
title_full MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
title_fullStr MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
title_full_unstemmed MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
title_sort MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
dc.creator.none.fl_str_mv Li, Minghui
Simonetti, Franco Lucio
Goncearenco, Alexander
Panchenko, Anna R.
author Li, Minghui
author_facet Li, Minghui
Simonetti, Franco Lucio
Goncearenco, Alexander
Panchenko, Anna R.
author_role author
author2 Simonetti, Franco Lucio
Goncearenco, Alexander
Panchenko, Anna R.
author2_role author
author
author
dc.subject.none.fl_str_mv PROTEIN PROTEIN INTERACTION
MUTATION
SEQUENCE VARIANTS
SERVER
topic PROTEIN PROTEIN INTERACTION
MUTATION
SEQUENCE VARIANTS
SERVER
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of impacts of variants on proteins. To address this need we introduce a new computational method MutaBind to evaluate the effects of sequence variants and disease mutations on protein interactions and calculate the quantitative changes in binding affinity. The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain optimization algorithms. The MutaBind server maps mutations on a structural protein complex, calculates the associated changes in binding affinity, determines the deleterious effect of a mutation, estimates the confidence of this prediction and produces a mutant structural model for download. MutaBind can be applied to a large number of problems, including determination of potential driver mutations in cancer and other diseases, elucidation of the effects of sequence variants on protein fitness in evolution and protein design. MutaBind is available at http://www.ncbi.nlm.nih.gov/projects/mutabind/.
Fil: Li, Minghui. National Institutes Of Health; Estados Unidos
Fil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina
Fil: Goncearenco, Alexander. National Institutes Of Health; Estados Unidos
Fil: Panchenko, Anna R.. National Institutes Of Health; Estados Unidos
description Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of impacts of variants on proteins. To address this need we introduce a new computational method MutaBind to evaluate the effects of sequence variants and disease mutations on protein interactions and calculate the quantitative changes in binding affinity. The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain optimization algorithms. The MutaBind server maps mutations on a structural protein complex, calculates the associated changes in binding affinity, determines the deleterious effect of a mutation, estimates the confidence of this prediction and produces a mutant structural model for download. MutaBind can be applied to a large number of problems, including determination of potential driver mutations in cancer and other diseases, elucidation of the effects of sequence variants on protein fitness in evolution and protein design. MutaBind is available at http://www.ncbi.nlm.nih.gov/projects/mutabind/.
publishDate 2016
dc.date.none.fl_str_mv 2016-05
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/11336/18159
Li, Minghui; Simonetti, Franco Lucio; Goncearenco, Alexander; Panchenko, Anna R.; MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions; Oxford University Press; Nucleic Acids Research; 44; W1; 5-2016; W494-501
0305-1048
1362-4962
CONICET Digital
CONICET
url http://hdl.handle.net/11336/18159
identifier_str_mv Li, Minghui; Simonetti, Franco Lucio; Goncearenco, Alexander; Panchenko, Anna R.; MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions; Oxford University Press; Nucleic Acids Research; 44; W1; 5-2016; W494-501
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/url/https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw374
info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkw374
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
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score 13.070432

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