title: CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.
abstract: BACKGROUND
  Recent breakthroughs in protein residue-residue contact prediction have made reliable de novo prediction of protein structures possible. The key was to apply statistical methods that can distinguish direct couplings between pairs of columns in a multiple sequence alignment from merely correlated pairs, i.e. to separate direct from indirect effects. Two classes of such methods exist, either relying on regularized inversion of the covariance matrix or on pseudo-likelihood maximization (PLM). Although PLM-based methods offer clearly higher precision, available tools are not sufficiently optimized and are written in interpreted languages that introduce additional overheads. This impedes the runtime and large-scale contact prediction for larger protein families, multi-domain proteins and protein-protein interactions.
  
  
  RESULTS
  Here we introduce CCMpred, our performance-optimized PLM implementation in C and CUDA C. Using graphics cards in the price range of current six-core processors, CCMpred can predict contacts for typical alignments 35-113 times faster and with the same precision as the most accurate published methods. For users without a CUDA-capable graphics card, CCMpred can also run in a CPU mode that is still 4-14 times faster. Thanks to our speed-ups (http://dictionary.cambridge.org/dictionary/british/speed-up) contacts for typical protein families can be predicted in 15-60 s on a consumer-grade GPU and 1-6 min on a six-core CPU.
  
  
  METHODS
  CCMpred is free and open-source software under the GNU Affero General Public License v3 (or later) available at https://bitbucket.org/soedinglab/ccmpred.
authors: Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors: Stefan
authors: S
authors: Seemayer
authors: Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors: Markus
authors: M
authors: Gruber
authors: Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors: Johannes
authors: J
authors: Söding
mesh_terms: D009154:Mutation; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins