title: bbcontacts: prediction of β-strand pairing from direct coupling patterns.
abstract: BACKGROUND
  It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. Here, we exploit the structural regularity of paired β-strands that leads to characteristic patterns in the noisy matrices of couplings. The β-β contacts should be detected more reliably than single contacts, reducing the required number of sequences in the MSAs.
  
  
  RESULTS
  bbcontacts predicts β-β contacts by detecting these characteristic patterns in the 2D map of coupling scores using two hidden Markov models (HMMs), one for parallel and one for antiparallel contacts. β-bulges are modelled as indel states. In contrast to existing methods, bbcontacts uses predicted instead of true secondary structure. On a standard set of 916 test proteins, 34% of which have MSAs with < 1000 sequences, bbcontacts achieves 50% precision for contacting β-β residue pairs at 50% recall using predicted secondary structure and 64% precision at 64% recall using true secondary structure, while existing tools achieve around 45% precision at 45% recall using true secondary structure.
  
  
  METHODS
  bbcontacts is open source software (GNU Affero GPL v3) available at https://bitbucket.org/soedinglab/bbcontacts .
authors.affiliation: Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Jessica
authors.initials: J
authors.lastname: Andreani
authors.affiliation: Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Söding
mesh_terms: D008390:Markov Chains; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software