{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T20:59:17Z","timestamp":1773435557346,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Accurate topology prediction of transmembrane \u03b2-barrels is still an open question. Here, we present BOCTOPUS2, an improved topology prediction method for transmembrane \u03b2-barrels that can also identify the barrel domain, predict the topology and identify the orientation of residues in transmembrane \u03b2-strands. The major novelty of BOCTOPUS2 is the use of the dyad-repeat pattern of lipid and pore facing residues observed in transmembrane \u03b2-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 \u03b2-barrel proteins.<\/jats:p>\n               <jats:p>Availability and implementation: BOCTOPUS2 webserver along with full dataset and source code is available at http:\/\/boctopus.bioinfo.se\/<\/jats:p>\n               <jats:p>Contact: arne@bioinfo.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw025","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T01:09:07Z","timestamp":1455498547000},"page":"1571-1573","source":"Crossref","is-referenced-by-count":78,"title":["Inclusion of dyad-repeat pattern improves topology prediction of transmembrane \u03b2-barrel proteins"],"prefix":"10.1093","volume":"32","author":[{"given":"Sikander","family":"Hayat","sequence":"first","affiliation":[{"name":"1 Memorial Sloan Kettering Cancer Center, New York City, NY, USA,"}]},{"given":"Christoph","family":"Peters","sequence":"additional","affiliation":[{"name":"2 Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and"}]},{"given":"Nanjiang","family":"Shu","sequence":"additional","affiliation":[{"name":"2 Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and"},{"name":"3 Sweden Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm University, Sweden"}]},{"given":"Konstantinos D.","family":"Tsirigos","sequence":"additional","affiliation":[{"name":"2 Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and"}]},{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"2 Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and"}]}],"member":"286","published-online":{"date-parts":[[2016,1,21]]},"reference":[{"key":"2023020112273586000_btw025-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped blast and psi-blast: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020112273586000_btw025-B2","doi-asserted-by":"crossref","first-page":"W400","DOI":"10.1093\/nar\/gkh417","article-title":"PRED-TMBB: a web server for predicting the topology of {beta}-barrel outer membrane proteins","volume":"32","author":"Bagos","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020112273586000_btw025-B3","doi-asserted-by":"crossref","first-page":"W186","DOI":"10.1093\/nar\/gkl262","article-title":"PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins","volume":"34","author":"Bigelow","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023020112273586000_btw025-B4","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"Uniprot: a hub for protein information","volume":"43","author":"Consortium","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020112273586000_btw025-B5","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1093\/bioinformatics\/btq308","article-title":"A highly accurate statistical approach for the prediction of transmembrane \u03b2-barrels","volume":"26","author":"Freeman","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020112273586000_btw025-B6","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1093\/bioinformatics\/btr710","article-title":"Boctopus: improved topology prediction of transmembrane \u03b2 barrel proteins","volume":"28","author":"Hayat","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112273586000_btw025-B7","doi-asserted-by":"crossref","first-page":"5413","DOI":"10.1073\/pnas.1419956112","article-title":"All-atom 3d structure prediction of transmembrane \u03b2-barrel proteins from sequences","volume":"112","author":"Hayat","year":"2015","journal-title":"Proc. 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