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dc.contributor.authorJiménez-García, Brian
dc.contributor.authorPons, Carles
dc.contributor.authorSvergun, Dmitri I.
dc.contributor.authorBernadó, Pau
dc.contributor.authorFernández-Recio, Juan
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2016-03-17T13:56:54Z
dc.date.available2016-03-17T13:56:54Z
dc.date.issued2015-07-01
dc.identifier.citationJiménez-García, Brian [et al.]. pyDockSAXS: protein–protein complex structure by SAXS and computational docking. "Nucleic Acids Research", 01 Juliol 2015, vol. 43, núm. W1, p. W356-W361.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/2117/84631
dc.description.abstractStructural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein–protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein–protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction.
dc.description.sponsorshipPrograma Estatal I+D+i, the SpanishMinistry of Economy andCompetitiveness [BIO2013-48213-R to J.F.-R.]; Agence Nationale de la Recherche [SPIN-HD-ANR-CHEX-2011 and ATIP-Avenir Program to P.B.]; FPU Fellowship, the Spanish Ministry of Science and Innovation [BES-2011-045634 to B.J.G.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BIO2013-48213-R]; Agence Nationale de la Recherche [SPIN-HDANR- CHEX-2011].
dc.format.extent6 p.
dc.language.isoeng
dc.publisherOxford Journals
dc.rightsAttribution-NonCommercial-NoDerivs 4.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/es/
dc.subjectÀrees temàtiques de la UPC::Enginyeria biomèdica
dc.subject.lcshProtein-protein interactions
dc.subject.otherProtein–protein interactions
dc.subject.otherSmall-angle X-ray scattering (SAXS)
dc.subject.otherFTDOCK
dc.titlepyDockSAXS: protein–protein complex structure by SAXS and computational docking
dc.typeArticle
dc.subject.lemacProteïnes--Enginyeria genètica
dc.identifier.doi10.1093/nar/gkv368
dc.relation.publisherversionhttp://nar.oxfordjournals.org/content/43/W1/W356.long
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO/1PE/BIO2013-48213-R
upcommons.citation.publishedtrue
upcommons.citation.publicationNameNucleic Acids Research
upcommons.citation.volume43
upcommons.citation.numberW1
upcommons.citation.startingPageW356
upcommons.citation.endingPageW361


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