Sikander Hayat1, Christoph Peters2, Nanjiang Shu3, Konstantinos D Tsirigos2, Arne Elofsson2. 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
UNLABELLED: : 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.
UNLABELLED: : 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.
Authors: Emily L Wynn; Matthew M Hille; John Dustin Loy; Gennie Schuller; Kristen L Kuhn; Aaron M Dickey; James L Bono; Michael L Clawson Journal: BMC Microbiol Date: 2022-10-21 Impact factor: 4.465
Authors: Melinda M Pettigrew; Christian P Ahearn; Janneane F Gent; Yong Kong; Mary C Gallo; James B Munro; Adonis D'Mello; Sanjay Sethi; Hervé Tettelin; Timothy F Murphy Journal: Proc Natl Acad Sci U S A Date: 2018-03-19 Impact factor: 11.205
Authors: Chaille T Webb; Dilini Chandrapala; Siti Nurbaya Oslan; Rebecca S Bamert; Rhys D Grinter; Rhys A Dunstan; Rebecca J Gorrell; Jiangning Song; Richard A Strugnell; Trevor Lithgow; Terry Kwok Journal: Microbiologyopen Date: 2017-10-21 Impact factor: 3.139