Predicting protein-protein interactions using BiGGER

Bibliographic Details
Main Author: Almeida, Rui Miguel Lourenço Rocha de
Publication Date: 2016
Other Authors: Dell'Acqua, Simone, Krippahl, Ludwig, Moura, José J. G., Pauleta, Sofia R.
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: https://doi.org/10.3390/molecules21081037
Summary: 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)
id RCAP_ca823583c8de3b9b401fe45a9a50af3c
oai_identifier_str oai:run.unl.pt:10362/21654
network_acronym_str RCAP
network_name_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository_id_str https://opendoar.ac.uk/repository/7160
spelling 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:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-22T17:26:20Zoai:run.unl.pt:10362/21654Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T16:57:38.200173Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
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:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
_version_ 1833596321888468992

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