{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T22:10:30Z","timestamp":1773871830758,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Transmembrane \u03b2 barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important.<\/jats:p>\n               <jats:p>Results: Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task.<\/jats:p>\n               <jats:p>Availability: BOCTOPUS is freely available as a web server at: http:\/\/boctopus.cbr.su.se\/. The datasets used for training and evaluations are also available from this site.<\/jats:p>\n               <jats:p>Contact: \u00a0arne@bioinfo.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr710","type":"journal-article","created":{"date-parts":[[2012,1,14]],"date-time":"2012-01-14T01:50:47Z","timestamp":1326505847000},"page":"516-522","source":"Crossref","is-referenced-by-count":69,"title":["BOCTOPUS: improved topology prediction of transmembrane \u03b2 barrel proteins"],"prefix":"10.1093","volume":"28","author":[{"given":"Sikander","family":"Hayat","sequence":"first","affiliation":[{"name":"Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, SciLifeLab, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden"}]},{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, SciLifeLab, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2012,1,13]]},"reference":[{"key":"2023012512182843400_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":"2023012512182843400_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 \u03b2-barrel outer membrane proteins","volume":"32","author":"Bagos","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012512182843400_B3","doi-asserted-by":"crossref","first-page":"0","DOI":"10.1186\/1471-2105-6-7","article-title":"Evaluation of methods for predicting the topology of \u03b2-barrel outer membrane proteins and a consensus prediction method","volume":"6","author":"Bagos","year":"2005","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 2","key":"2023012512182843400_B4","doi-asserted-by":"crossref","first-page":"W394","DOI":"10.1093\/nar\/gkh351","article-title":"BOMP: a program to predict integral \u03b2-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria","volume":"32","author":"Berven","year":"2004","journal-title":"Nucleic Acids Res."},{"issue":"Suppl. 2","key":"2023012512182843400_B5","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":"2023012512182843400_B6","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.compbiolchem.2004.02.004","article-title":"Scoring hidden Markov models to discriminate [beta]-barrel membrane proteins","volume":"28","author":"Deng","year":"2004","journal-title":"Comput. 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