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BMC Bioinformatics. 2014 Mar 26;15:85. doi: 10.1186/1471-2105-15-85.

FreeContact: fast and free software for protein contact prediction from residue co-evolution.

Author information

1
Department for Bioinformatics and Computational Biology, TU Munich, Boltzmannstraße 3, Garching 85748, Germany. assistant@rostlab.org.

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).

PMID:
24669753
PMCID:
PMC3987048
DOI:
10.1186/1471-2105-15-85
[Indexed for MEDLINE]
Free PMC Article

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