{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T09:50:19Z","timestamp":1722678619862},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Transmembrane \u03b2-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few \u03b2-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful.<\/jats:p>\n               <jats:p>Results: Here, we present tobmodel; a method for generating 3D models of \u03b2-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the \u03b2-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average error of 1.61 \u00c5. Tobmodel predicts the correct topology for 75% of the proteins in the dataset which is a slight improvement over BOCTOPUS alone. More importantly, however, tobmodel provides a C\u03b1 template with an average RMSD of 7.24 \u00c5 from the native structure.<\/jats:p>\n               <jats:p>Availability: Tobmodel is freely available as a web server at: http:\/\/tobmodel.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>","DOI":"10.1093\/bioinformatics\/bts233","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i90-i96","source":"Crossref","is-referenced-by-count":14,"title":["Ranking models of transmembrane <i>\u03b2<\/i>-barrel proteins using Z-coordinate predictions"],"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, Science for Life Laboratory, 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, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512384072600_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":"2023012512384072600_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":"2023012512384072600_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"},{"key":"2023012512384072600_B4","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.tibs.2011.11.004","article-title":"Mitochondrial protein import: from transport pathways to an integrated network","volume":"37","author":"Becker","year":"2012","journal-title":"Trends Biochem. 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Protein Peptide Sci."},{"key":"2023012512384072600_B10","doi-asserted-by":"crossref","first-page":"e191","DOI":"10.1093\/bioinformatics\/btl206","article-title":"Zpred: predicting the distance to the membrane center for residues in \u03b1-helical membrane proteins","volume":"22","author":"Granseth","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512384072600_B11","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1002\/jcc.10386","article-title":"Neural network-based prediction of transmembrane \u03b2-strand segments in outer membrane proteins","volume":"25","author":"Gromiha","year":"2004","journal-title":"J. Comput. 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