Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins

Bioinformatics. 2016 May 15;32(10):1571-3. doi: 10.1093/bioinformatics/btw025. Epub 2016 Jan 21.


: 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.

Availability and implementation: BOCTOPUS2 webserver along with full dataset and source code is available at

Contact: :

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Computational Biology
  • Membrane Proteins / chemistry*
  • Models, Molecular
  • Programming Languages
  • Protein Structure, Secondary


  • Membrane Proteins