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Title | FreeContact: fast and free software for protein contact prediction from residue co-evolution. |
Publication Type | Journal Article |
Year of Publication | 2014 |
Authors | Kaján, L, Hopf, TA, Kalaš, M, Marks, DS, Rost, B |
Journal | BMC Bioinformatics |
Volume | 15 |
Pagination | 85 |
Date Published | 2014 |
ISSN | 1471-2105 |
Keywords | Algorithms, Computational Biology, Protein Conformation, Proteins, Sequence Analysis, Protein, Software |
Abstract | 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). |
DOI | 10.1186/1471-2105-15-85 |
Alternate Journal | BMC Bioinformatics |
PubMed ID | 24669753 |
PubMed Central ID | PMC3987048 |
Grant List | R01 GM106303 / GM / NIGMS NIH HHS / United States |