Predicting protein-protein interactions using BiGGER
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://doi.org/10.3390/molecules21081037 |
Resumo: | Fundacao para a Ciencia e Tecnologia (FCT) - PTDC/EIA-CCO/115999/2009; PTDC/BIAPRO/098882/2008; PTDC/BIA-PRO/109796/2009; PTDC/QUI-BIQ/116481/2010 ; FCT-ANR/BBB-BQB/0023/2012; SFRH/BPD/80293/2011; Unidade de Ciencias Biomoleculares Aplicadas-UCIBIO - FCT/MEC (UID/Multi/04378/2013); ERDF (POCI-01-0145-FEDER-007728) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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Predicting protein-protein interactions using BiGGERCase studiesBiGGERDockingElectron transfer complexesMolecular recognitionNMRProtein-protein interactionsOrganic ChemistryFundacao para a Ciencia e Tecnologia (FCT) - PTDC/EIA-CCO/115999/2009; PTDC/BIAPRO/098882/2008; PTDC/BIA-PRO/109796/2009; PTDC/QUI-BIQ/116481/2010 ; FCT-ANR/BBB-BQB/0023/2012; SFRH/BPD/80293/2011; Unidade de Ciencias Biomoleculares Aplicadas-UCIBIO - FCT/MEC (UID/Multi/04378/2013); ERDF (POCI-01-0145-FEDER-007728)The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A) in which no specific contact data is available; (Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.DQ - Departamento de QuímicaUCIBIO - Applied Molecular Biosciences UnitDI - Departamento de InformáticaCENTRIA – Centro de Inteligência ArtificialRUNAlmeida, Rui Miguel Lourenço Rocha deDell'Acqua, SimoneKrippahl, LudwigMoura, José J. G.Pauleta, Sofia R.2017-06-21T22:02:19Z2016-08-012016-08-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://doi.org/10.3390/molecules21081037engPURE: 1302832http://www.scopus.com/inward/record.url?scp=84983320407&partnerID=8YFLogxKhttps://doi.org/10.3390/molecules21081037info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:08:34Zoai:run.unl.pt:10362/21654Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:26:54.934700Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Predicting protein-protein interactions using BiGGER Case studies |
title |
Predicting protein-protein interactions using BiGGER |
spellingShingle |
Predicting protein-protein interactions using BiGGER Almeida, Rui Miguel Lourenço Rocha de BiGGER Docking Electron transfer complexes Molecular recognition NMR Protein-protein interactions Organic Chemistry |
title_short |
Predicting protein-protein interactions using BiGGER |
title_full |
Predicting protein-protein interactions using BiGGER |
title_fullStr |
Predicting protein-protein interactions using BiGGER |
title_full_unstemmed |
Predicting protein-protein interactions using BiGGER |
title_sort |
Predicting protein-protein interactions using BiGGER |
author |
Almeida, Rui Miguel Lourenço Rocha de |
author_facet |
Almeida, Rui Miguel Lourenço Rocha de Dell'Acqua, Simone Krippahl, Ludwig Moura, José J. G. Pauleta, Sofia R. |
author_role |
author |
author2 |
Dell'Acqua, Simone Krippahl, Ludwig Moura, José J. G. Pauleta, Sofia R. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
DQ - Departamento de Química UCIBIO - Applied Molecular Biosciences Unit DI - Departamento de Informática CENTRIA – Centro de Inteligência Artificial RUN |
dc.contributor.author.fl_str_mv |
Almeida, Rui Miguel Lourenço Rocha de Dell'Acqua, Simone Krippahl, Ludwig Moura, José J. G. Pauleta, Sofia R. |
dc.subject.por.fl_str_mv |
BiGGER Docking Electron transfer complexes Molecular recognition NMR Protein-protein interactions Organic Chemistry |
topic |
BiGGER Docking Electron transfer complexes Molecular recognition NMR Protein-protein interactions Organic Chemistry |
description |
Fundacao para a Ciencia e Tecnologia (FCT) - PTDC/EIA-CCO/115999/2009; PTDC/BIAPRO/098882/2008; PTDC/BIA-PRO/109796/2009; PTDC/QUI-BIQ/116481/2010 ; FCT-ANR/BBB-BQB/0023/2012; SFRH/BPD/80293/2011; Unidade de Ciencias Biomoleculares Aplicadas-UCIBIO - FCT/MEC (UID/Multi/04378/2013); ERDF (POCI-01-0145-FEDER-007728) |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-08-01 2016-08-01T00:00:00Z 2017-06-21T22:02:19Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.3390/molecules21081037 |
url |
https://doi.org/10.3390/molecules21081037 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
PURE: 1302832 http://www.scopus.com/inward/record.url?scp=84983320407&partnerID=8YFLogxK https://doi.org/10.3390/molecules21081037 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799137898352607232 |