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

• Published in: BMC bioinformatics Vol. 15; no. 1; p. 85
• Main Authors: Kaján, László, Hopf, Thomas A, Kalaš, Matúš, Marks, Debora S, Rost, Burkhard
• Format: Journal Article
• Language: English
• Published: London BioMed Central 26.03.2014; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Bioinformatics; Biology; Biomedical and Life Sciences; C plus plus; Colleges & universities; Computational Biology - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Internet service providers; Life Sciences; Methods; Microarrays; Programming languages; Protein Conformation; Protein structure prediction; Proteins; Proteins - chemistry; Proteins - genetics; Public software; Sequence analysis (applications); Sequence Analysis, Protein - methods; Software; Technology application; EVcouplings; PSICOV; mfDCA; EVfold; 2D prediction; Open-source software; Protein structure prediction; BioXSD; Debian package; Protein sequence analysis; Fast protein contact prediction
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-15-85

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).