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

BMC Bioinformatics

László Kaján³  Thomas A Hopf¹  Matúš Kalaš⁴  Debora S Marks¹  Burkhard Rost² 

[1] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA

[2] WZW – Weihenstephan, Alte Akademie 8, Freising, Germany

[3] Department for Bioinformatics and Computational Biology, TU Munich, Boltzmannstraße 3, Garching 85748, Germany

[4] Department of Informatics, University of Bergen, Bergen 5008, Norway

关键词: Debian package;    BioXSD;    mfDCA;    PSICOV;    EVcouplings;    EVfold;    Open-source software;    2D prediction;    Fast protein contact prediction;    Protein sequence analysis;    Protein structure prediction;   

Others  :  1087584
DOI  :  10.1186/1471-2105-15-85

 received in 2013-09-30, accepted in 2014-03-18,  发布年份 2014

【 摘 要 】

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).

【 授权许可】

   
2014 Kaján et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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