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dc.contributor.authorKaján, László
dc.contributor.authorHopf, Thomas A.
dc.contributor.authorKalaš, Matúš
dc.contributor.authorMarks, Debora S.
dc.contributor.authorRost, Burkhard
dc.date.accessioned2016-01-20T11:44:06Z
dc.date.available2016-01-20T11:44:06Z
dc.date.issued2014-03-26
dc.PublishedBMC Bioinformatics 2014, 15(1:85)eng
dc.identifier.issn1471-2105en_US
dc.identifier.urihttps://hdl.handle.net/1956/10995
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 BY 2.0eng
dc.rights.urihttp://creativecommons.org/licenses/by/2.0eng
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.updated2015-11-25T12:32:55Z
dc.description.versionpublishedVersionen_US
dc.rights.holderCopyright Kaján et al.; licensee BioMed Central Ltd. 2014en_US
dc.identifier.doihttps://doi.org/10.1186/1471-2105-15-85
dc.identifier.cristin1153112
dc.subject.nsiVDP::Matematikk og naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475
dc.subject.nsiVDP::Mathematics and natural scienses: 400::Basic biosciences: 470::Bioinformatics: 475
dc.subject.nsiVDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470en_US
dc.subject.nsiVDP::Teknologi: 500::Informasjons- og kommunikasjonsteknologi: 550en_US


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Attribution CC BY 2.0
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