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

Sikander Hayat | Zendy; Christoph Peters | Zendy; Nanjiang Shu | Zendy; Konstantinos D. Tsirigos | Zendy; Arne Elofsson | Zendy

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

Author(s) -

Sikander Hayat,

Christoph Peters,

Nanjiang Shu,

Konstantinos D. Tsirigos,

Arne Elofsson

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw025

Subject(s) - transmembrane protein , barrel (horology) , topology (electrical circuits) , transmembrane domain , computer science , membrane topology , benchmark (surveying) , protein structure prediction , protein structure , biology , mathematics , amino acid , engineering , genetics , biochemistry , mechanical engineering , receptor , geodesy , combinatorics , geography

: 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.

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