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

Bioinformatics
Sikander HayatArne Elofsson

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. BOCTOPUS2 webserver along with full dataset and source code is available at http://boctopus.bioinfo.se/ : arne@bioinfo.se Supplementary data are available at Bioinformatics online.

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Citations

Sep 3, 2016·Bioinformatics·Konstantinos D TsirigosPantelis G Bagos
Sep 11, 2018·Acta Crystallographica. Section D, Structural Biology·Javier Abellón-RuizBert van den Berg
Nov 30, 2018·ELife·Meghan Whitney FranklinJoanna Sg Slusky
Jan 18, 2018·Nature Communications·Anuwat AunkhamBert van den Berg
Nov 28, 2017·Nature Biotechnology·Mohan BabuAndrew Emili
Jun 15, 2017·Frontiers in Microbiology·Peili CaoLiandong Qu
Mar 21, 2018·Proceedings of the National Academy of Sciences of the United States of America·Melinda M PettigrewTimothy F Murphy
Mar 27, 2019·Nature Communications·Nuria Gómez-SantosLotte Søgaard-Andersen
Aug 14, 2020·BMC Microbiology·Michael L ClawsonTimothy P L Smith
Jan 31, 2018·Proceedings of the National Academy of Sciences of the United States of America·Wei TianHammad Naveed
Oct 27, 2018·MicrobiologyOpen·Małgorzata RyngajłłoStanisław Bielecki
May 24, 2019·The Protein Journal·Henrik NielsenGunnar von Heijne
Jul 13, 2019·Frontiers in Immunology·Karina A PasquevichJuliana Cassataro
Mar 23, 2017·Proceedings of the National Academy of Sciences of the United States of America·Pengbo Cao, Daniel Wall
Apr 27, 2021·Computational and Structural Biotechnology Journal·Xinjie HuiYejun Wang
Sep 3, 2021·Acta Crystallographica. Section D, Structural Biology·Joana Pereira, Vikram Alva

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