Journal
BMC BIOINFORMATICS
Volume 15, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/1471-2105-15-85
Keywords
Protein structure prediction; Protein sequence analysis; Fast protein contact prediction; 2D prediction; Open-source software; EVfold; EVcouplings; PSICOV; mfDCA; BioXSD; Debian package
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Funding
- Alexander von Humboldt Foundation through the German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung)
- Research Council of Norway [208481]
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Background: 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).
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