title: FreeContact: fast and free software for protein contact prediction from residue co-evolution.
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).
authors.forename: László
authors.initials: L
authors.lastname: Kaján
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Hopf
authors.forename: Matúš
authors.initials: M
authors.lastname: Kalaš
authors.forename: Debora S
authors.initials: DS
authors.lastname: Marks
authors.affiliation: Department for Bioinformatics and Computational Biology, TU Munich, Boltzmannstraße 3, Garching 85748, Germany. assistant@rostlab.org.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins