Inclusion of dyad-repeat pattern improves topology prediction of transmembrane beta-barrel proteins
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
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.
Biochemistry and Molecular Biology Bioinformatics (Computational Biology)
IdentifiersURN: urn:nbn:se:su:diva-131992DOI: 10.1093/bioinformatics/btw025ISI: 000376656900022PubMedID: 26794316OAI: oai:DiVA.org:su-131992DiVA: diva2:952690