Vis enkel innførsel

dc.contributor.authorKaján, Lászlóeng
dc.contributor.authorHopf, Thomas A.eng
dc.contributor.authorKalaš, Matúšeng
dc.contributor.authorMarks, Debora S.eng
dc.contributor.authorRost, Burkhardeng
dc.date.accessioned2014-10-07T13:47:08Z
dc.date.available2014-10-07T13:47:08Z
dc.date.issued2014-03-26eng
dc.identifier.issn1471-2105en_US
dc.identifier.urihttps://hdl.handle.net/1956/8604
dc.description.abstractBackground: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein three-dimensional structure. The method EVfold broke new ground using mean-field Direct Coupling Analysis (EVfold-mfDCA); the method PSICOV applied a related concept by estimating a sparse inverse covariance matrix. Both methods (EVfold-mfDCA and PSICOV) are publicly available, but both require too much CPU time for interactive applications. On top, EVfold-mfDCA depends on proprietary software. Results: Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library “libfreecontact”, complete with command line tool “freecontact”, as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability. Conclusions: FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud).en_US
dc.language.isoengeng
dc.publisherBioMed Centralen_US
dc.rightsAttribution CC BYeng
dc.rights.urihttp://creativecommons.org/licenses/by/2.0eng
dc.subjectProtein structure predictioneng
dc.subjectProtein sequence analysiseng
dc.subjectFast protein contact predictioneng
dc.subject2D predictioneng
dc.subjectOpen-source softwareeng
dc.subjectEVfoldeng
dc.subjectEVcouplingseng
dc.subjectPSICOVeng
dc.subjectmfDCAeng
dc.subjectBioXSDeng
dc.subjectDebian packageeng
dc.titleFreeContact: fast and free software for protein contact prediction from residue co-evolutionen_US
dc.typePeer reviewed
dc.typeJournal article
dc.date.updated2014-04-22T03:32:26Z
dc.description.versionPeer Reviewed
dc.description.versionpublishedVersionen_US
dc.rights.holderLászló Kaján et al.; licensee BioMed Central Ltd.en_US
dc.rights.holderCopyright 2014 Kaján et al.; licensee BioMed Central Ltd.en_US
dc.source.articlenumber85
dc.identifier.doihttps://doi.org/10.1186/1471-2105-15-85
dc.identifier.cristin1153112
dc.source.journalBMC Bioinformatics
dc.source.4015


Tilhørende fil(er)

Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail
Thumbnail

Denne innførselen finnes i følgende samling(er)

Vis enkel innførsel

Attribution CC BY
Med mindre annet er angitt, så er denne innførselen lisensiert som Attribution CC BY