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

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

Author information

1
Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
2
Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and.
3
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.

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.

AVAILABILITY AND IMPLEMENTATION:

BOCTOPUS2 webserver along with full dataset and source code is available at http://boctopus.bioinfo.se/

CONTACT:

: arne@bioinfo.se

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26794316
DOI:
10.1093/bioinformatics/btw025
[Indexed for MEDLINE]

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