Structural characterization of protein–protein interactions with pyDockSAXS

Structural characterization of protein–protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fractio...

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Detalles Bibliográficos
Autores: Jiménez-García, Brian, Bernadó, Pau, Fernández-Recio, Juan
Tipo de recurso: capítulo de libro
Fecha de publicación:2020
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/345725
Acceso en línea:https://hdl.handle.net/2117/345725
https://dx.doi.org/10.1007/978-1-0716-0270-6_10
Access Level:acceso abierto
Palabra clave:Protein-protein interactions.
Protein conformation
Protein–protein interactions
Structural modeling
Small-angle X-ray scattering (SAXS)
Computational docking
FTDock
CRYSOL
pyDock
Proteïnes -- Anàlisi -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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oai_identifier_str oai:upcommons.upc.edu:2117/345725
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spelling Structural characterization of protein–protein interactions with pyDockSAXSJiménez-García, BrianBernadó, PauFernández-Recio, JuanProtein-protein interactions.Protein conformationProtein–protein interactionsStructural modelingSmall-angle X-ray scattering (SAXS)Computational dockingFTDockCRYSOLpyDockProteïnes -- Anàlisi -- InformàticaÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaStructural characterization of protein–protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fraction of all possible protein–protein interactions, due to the technical limitations of high-resolution structural determination methods. In this context, low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be combined with computational docking to provide structural models of protein–protein interactions at large scale. In this chapter, we describe the pyDockSAXS web server (https://life.bsc.es/pid/pydocksaxs), which uses pyDock docking and scoring to provide structural models that optimally satisfy the input SAXS data. This server, which is freely available to the scientific community, provides an automatic pipeline to model the structure of a protein–protein complex from SAXS dataThis work was supported by the Spanish Ministry of Science (grant BIO2016-79930-R), the European Union H2020 programme (grant MuG 676566), and the Labex EpiGenMed, an "Investissements d’avenir" program (ANR-10-LABX-12-01). The CBS is a member of France-BioImaging (FBI) and the French Infrastructure for Integrated Structural Biology (FRISBI), two national infrastructures supported by the French National Research Agency (ANR-10-INSB-04-01 and ANR-10-INSB-05, respectively).Peer ReviewedHumana PressGáspári, Z.20202020-01-0120212021-05-17book parthttp://purl.org/coar/resource_type/c_3248AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/bookPartapplication/pdfhttps://hdl.handle.net/2117/345725https://dx.doi.org/10.1007/978-1-0716-0270-6_1032006283reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3457252026-05-27T15:37:01Z
dc.title.none.fl_str_mv Structural characterization of protein–protein interactions with pyDockSAXS
title Structural characterization of protein–protein interactions with pyDockSAXS
spellingShingle Structural characterization of protein–protein interactions with pyDockSAXS
Jiménez-García, Brian
Protein-protein interactions.
Protein conformation
Protein–protein interactions
Structural modeling
Small-angle X-ray scattering (SAXS)
Computational docking
FTDock
CRYSOL
pyDock
Proteïnes -- Anàlisi -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
title_short Structural characterization of protein–protein interactions with pyDockSAXS
title_full Structural characterization of protein–protein interactions with pyDockSAXS
title_fullStr Structural characterization of protein–protein interactions with pyDockSAXS
title_full_unstemmed Structural characterization of protein–protein interactions with pyDockSAXS
title_sort Structural characterization of protein–protein interactions with pyDockSAXS
dc.creator.none.fl_str_mv Jiménez-García, Brian
Bernadó, Pau
Fernández-Recio, Juan
author Jiménez-García, Brian
author_facet Jiménez-García, Brian
Bernadó, Pau
Fernández-Recio, Juan
author_role author
author2 Bernadó, Pau
Fernández-Recio, Juan
author2_role author
author
dc.contributor.none.fl_str_mv Gáspári, Z.
dc.subject.none.fl_str_mv Protein-protein interactions.
Protein conformation
Protein–protein interactions
Structural modeling
Small-angle X-ray scattering (SAXS)
Computational docking
FTDock
CRYSOL
pyDock
Proteïnes -- Anàlisi -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
topic Protein-protein interactions.
Protein conformation
Protein–protein interactions
Structural modeling
Small-angle X-ray scattering (SAXS)
Computational docking
FTDock
CRYSOL
pyDock
Proteïnes -- Anàlisi -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
description Structural characterization of protein–protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fraction of all possible protein–protein interactions, due to the technical limitations of high-resolution structural determination methods. In this context, low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be combined with computational docking to provide structural models of protein–protein interactions at large scale. In this chapter, we describe the pyDockSAXS web server (https://life.bsc.es/pid/pydocksaxs), which uses pyDock docking and scoring to provide structural models that optimally satisfy the input SAXS data. This server, which is freely available to the scientific community, provides an automatic pipeline to model the structure of a protein–protein complex from SAXS data
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-01-01
2021
2021-05-17
dc.type.none.fl_str_mv book part
http://purl.org/coar/resource_type/c_3248
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/bookPart
format bookPart
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/345725
https://dx.doi.org/10.1007/978-1-0716-0270-6_10
32006283
url https://hdl.handle.net/2117/345725
https://dx.doi.org/10.1007/978-1-0716-0270-6_10
identifier_str_mv 32006283
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Humana Press
publisher.none.fl_str_mv Humana Press
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869416252590522368
score 15,300719

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