title: Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
abstract: : Accurate topology prediction of transmembrane β-barrels is still an open question. Here, we present BOCTOPUS2, an improved topology prediction method for transmembrane β-barrels that can also identify the barrel domain, predict the topology and identify the orientation of residues in transmembrane β-strands. The major novelty of BOCTOPUS2 is the use of the dyad-repeat pattern of lipid and pore facing residues observed in transmembrane β-barrels. In a cross-validation test on a benchmark set of 42 proteins, BOCTOPUS2 predicts the correct topology in 69% of the proteins, an improvement of more than 10% over the best earlier method (BOCTOPUS) and in addition, it produces significantly fewer erroneous predictions on non-transmembrane β-barrel proteins.
  
  
  
  BOCTOPUS2 webserver along with full dataset and source code is available at http://boctopus.bioinfo.se/
  
  
  
  : arne@bioinfo.se
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
authors.forename: Sikander
authors.initials: S
authors.lastname: Hayat
authors.affiliation: Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and.
authors.forename: Christoph
authors.initials: C
authors.lastname: Peters
authors.affiliation: Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and Sweden Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm University, Sweden.
authors.forename: Nanjiang
authors.initials: N
authors.lastname: Shu
authors.affiliation: Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and.
authors.forename: Konstantinos D
authors.initials: KD
authors.lastname: Tsirigos
authors.affiliation: Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and.
authors.forename: Arne
authors.initials: A
authors.lastname: Elofsson
mesh_terms: D019295:Computational Biology; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011381:Programming Languages; D017433:Protein Structure, Secondary
chemical_list: D008565:Membrane Proteins