Building protein-protein interaction networks for Leishmania species through protein structural information

Detalhes bibliográficos
Autor(a) principal: Vasconcelos, Crhisllane Rafaele dos Santos
Data de Publicação: 2018
Outros Autores: Campos, Túlio de Lima, Rezende, Antonio Mauro
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/33069
Resumo: CNPq and CAPES agency.
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spelling Vasconcelos, Crhisllane Rafaele dos SantosCampos, Túlio de LimaRezende, Antonio Mauro2019-05-14T16:21:16Z2019-05-14T16:21:16Z2018VASCONCELOS, Crhisllane Rafaele dos Santos; CAMPOS, Túlio de Lima; REZENDE, Antonio Mauro. Building protein-protein interaction networks for Leishmania species through protein structural information. BMC Bioinformatics, v. 19, p. 1-13, Mar. 2018.1471-2105https://www.arca.fiocruz.br/handle/icict/3306910.1186/s12859-018-2105-6CNPq and CAPES agency.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Microbiologia. Recife, PE, Brasil / Universidade Federal de Pernambuco. Departamento de Genética. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Microbiologia. Recife, PE, Brasil / Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Plataforma de Bioinformática. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Microbiologia. Recife, PE, Brasil / Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Plataforma de Bioinformática. Recife, PE, Brasil / Universidade Federal de Pernambuco. Departamento de Genética. Recife, PE, Brasil.BACKGROUND: Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum. These parasites cause Leishmaniasis, a worldwide distributed and neglected disease, with limited treatment options using currently available drugs. RESULTS: The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. Our final model obtained an AUC = 0.88, with recall = 0.69, specificity = 0.88 and precision = 0.83. Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis, and 708 protein structures and 7391 protein interactions for L. infantum. The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. CONCLUSIONS: The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported.engBuilding protein-protein interaction networks for Leishmania species through protein structural informationinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleArea Under CurveLeishmaniasisMachine LearningProtein Interaction MapsProtozoanThermodynamicsÁrea Sob CurvaLeishmania / metabolismoLeishmaniose / metabolismoLeishmaniose / parasitologiaAprendizado de MáquinaMapas de Interação de ProteínaProteoma / metabolismoProteínas de protozoários / químicaTermodinâmicainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83094https://www.arca.fiocruz.br/bitstream/icict/33069/1/license.txtee3692f7b0b97d5638099ab94397d05fMD51ORIGINALBuilding protein-protein interaction networks for Leishmania species through protein structural information.pdfBuilding protein-protein interaction networks for Leishmania species through protein structural information.pdfapplication/pdf3619561https://www.arca.fiocruz.br/bitstream/icict/33069/2/Building%20protein-protein%20interaction%20networks%20for%20Leishmania%20species%20through%20protein%20structural%20information.pdf79a6e59308d77097b79f2fe26b68a238MD52TEXTBuilding protein-protein interaction networks for Leishmania species through protein structural information.pdf.txtBuilding protein-protein interaction networks for Leishmania species through protein structural information.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv Building protein-protein interaction networks for Leishmania species through protein structural information
title Building protein-protein interaction networks for Leishmania species through protein structural information
spellingShingle Building protein-protein interaction networks for Leishmania species through protein structural information
Vasconcelos, Crhisllane Rafaele dos Santos
Area Under Curve
Leishmaniasis
Machine Learning
Protein Interaction Maps
Protozoan
Thermodynamics
Área Sob Curva
Leishmania / metabolismo
Leishmaniose / metabolismo
Leishmaniose / parasitologia
Aprendizado de Máquina
Mapas de Interação de Proteína
Proteoma / metabolismo
Proteínas de protozoários / química
Termodinâmica
title_short Building protein-protein interaction networks for Leishmania species through protein structural information
title_full Building protein-protein interaction networks for Leishmania species through protein structural information
title_fullStr Building protein-protein interaction networks for Leishmania species through protein structural information
title_full_unstemmed Building protein-protein interaction networks for Leishmania species through protein structural information
title_sort Building protein-protein interaction networks for Leishmania species through protein structural information
author Vasconcelos, Crhisllane Rafaele dos Santos
author_facet Vasconcelos, Crhisllane Rafaele dos Santos
Campos, Túlio de Lima
Rezende, Antonio Mauro
author_role author
author2 Campos, Túlio de Lima
Rezende, Antonio Mauro
author2_role author
author
dc.contributor.author.fl_str_mv Vasconcelos, Crhisllane Rafaele dos Santos
Campos, Túlio de Lima
Rezende, Antonio Mauro
dc.subject.en.pt_BR.fl_str_mv Area Under Curve
Leishmaniasis
Machine Learning
Protein Interaction Maps
Protozoan
Thermodynamics
topic Area Under Curve
Leishmaniasis
Machine Learning
Protein Interaction Maps
Protozoan
Thermodynamics
Área Sob Curva
Leishmania / metabolismo
Leishmaniose / metabolismo
Leishmaniose / parasitologia
Aprendizado de Máquina
Mapas de Interação de Proteína
Proteoma / metabolismo
Proteínas de protozoários / química
Termodinâmica
dc.subject.decs.pt_BR.fl_str_mv Área Sob Curva
Leishmania / metabolismo
Leishmaniose / metabolismo
Leishmaniose / parasitologia
Aprendizado de Máquina
Mapas de Interação de Proteína
Proteoma / metabolismo
Proteínas de protozoários / química
Termodinâmica
description CNPq and CAPES agency.
publishDate 2018
dc.date.issued.fl_str_mv 2018
dc.date.accessioned.fl_str_mv 2019-05-14T16:21:16Z
dc.date.available.fl_str_mv 2019-05-14T16:21:16Z
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.citation.fl_str_mv VASCONCELOS, Crhisllane Rafaele dos Santos; CAMPOS, Túlio de Lima; REZENDE, Antonio Mauro. Building protein-protein interaction networks for Leishmania species through protein structural information. BMC Bioinformatics, v. 19, p. 1-13, Mar. 2018.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/33069
dc.identifier.issn.pt_BR.fl_str_mv 1471-2105
dc.identifier.doi.none.fl_str_mv 10.1186/s12859-018-2105-6
identifier_str_mv VASCONCELOS, Crhisllane Rafaele dos Santos; CAMPOS, Túlio de Lima; REZENDE, Antonio Mauro. Building protein-protein interaction networks for Leishmania species through protein structural information. BMC Bioinformatics, v. 19, p. 1-13, Mar. 2018.
1471-2105
10.1186/s12859-018-2105-6
url https://www.arca.fiocruz.br/handle/icict/33069
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
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collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/33069/1/license.txt
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