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dc.contributor.authorMoal, Iain H.
dc.contributor.authorBarradas-Bautista, Didier
dc.contributor.authorJiménez-Garcia, Brian
dc.contributor.authorTorchala, Mieczyslaw
dc.contributor.authorvan der Velde, Arjan
dc.contributor.authorVreven, Thom
dc.contributor.authorWeng, Zhiping
dc.contributor.authorBates, Paul A.
dc.contributor.authorFernández-Recio, Juan
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2017-07-25T13:11:19Z
dc.date.available2017-07-25T13:11:19Z
dc.date.issued2017-02-14
dc.identifier.citationMoal, I. H. [et al.]. IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. "Bioinformatics", 14 Febrer 2017, vol. 33, núm. 12, p. 1806-1813.
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/2117/106834
dc.description.abstractMotivation: In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Results: Atomic modeling of protein–protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. Availability and Implementation: IRaPPA has been implemented in the SwarmDock server (http://bmm.crick.ac.uk/∼SwarmDock/), pyDock server (http://life.bsc.es/pid/pydockrescoring/) and ZDOCK server (http://zdock.umassmed.edu/), with code available on request.
dc.description.sponsorshipThis work was supported by the European Molecular Biology Laboratory [I.H.M.]; the European Commission [Marie Curie Actions PIEF-GA-2012-327899 to I.H.M.]; the Biotechnology and Biological Sciences Research Council [Future Leader Fellowship BB/N011600/1 to I.H.M.]; Consejo Nacional de Ciencia y Tecnología [217686 to D.B.]; The Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001003), the UK Medical Research Council (FC001003) and the Wellcome Trust (FC001003) [M.T., P.A.B.]; Ministerio de Economía y Competitividad [FPI fellowship to B.J.G., IþDþI Research Project BIO2013-48213-R to J.F.R.]; and National Institutes of Health [R01 GM116960 to ZW].
dc.language.isoeng
dc.publisherOxford University Press
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 interactions
dc.subject.lcshMolecular biology
dc.subject.otherProtein–protein interactions (PPIs)
dc.subject.otherAtomic modeling
dc.subject.otherIRaPPA (Integrative Ranking of Protein–Protein Assemblies)
dc.titleIRaPPA: information retrieval based integration of biophysical models for protein assembly selection
dc.typeArticle
dc.subject.lemacProteïnes--Anàlisi
dc.subject.lemacBiologia molecular
dc.identifier.doi10.1093/bioinformatics/btx068
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttps://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx068
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO/1PE/BIO2013-48213-R
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/327899/EU/Exploring the evolution of protein-protein interactions and their networks using biophysical models/EEPPIBM
local.citation.publicationNameBioinformatics
local.citation.volume33
local.citation.number12
local.citation.startingPage1806
local.citation.endingPage1813


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