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Inclusion of dyad-repeat pattern improves topology prediction of transmembrane beta-barrel proteins
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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Number of Authors: 5
2016 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 32, no 10, 1571-1573 p.Article in journal (Refereed) Published
Abstract [en]

Accurate topology prediction of transmembrane beta-barrels is still an open question. Here, we present BOCTOPUS2, an improved topology prediction method for transmembrane beta-barrels that can also identify the barrel domain, predict the topology and identify the orientation of residues in transmembrane beta-strands. The major novelty of BOCTOPUS2 is the use of the dyad-repeat pattern of lipid and pore facing residues observed in transmembrane beta-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 beta-barrel proteins.

Place, publisher, year, edition, pages
2016. Vol. 32, no 10, 1571-1573 p.
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Biochemistry and Molecular Biology Bioinformatics (Computational Biology)
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URN: urn:nbn:se:su:diva-131992DOI: 10.1093/bioinformatics/btw025ISI: 000376656900022PubMedID: 26794316OAI: oai:DiVA.org:su-131992DiVA: diva2:952690
Available from: 2016-08-15 Created: 2016-07-05 Last updated: 2016-08-15Bibliographically approved

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Peters, ChristophShu, NanjiangTsirigos, Konstantinos D.Elofsson, Arne
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Department of Biochemistry and BiophysicsScience for Life Laboratory (SciLifeLab)
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