{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T15:50:44Z","timestamp":1762444244568},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1999,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: State-of-the-art methods for topology of \u03b1-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but \u223c6% worse than the best method that is utilizing multiple sequence alignments.<\/jats:p>\n               <jats:p>Availability and Implementation: TOPCONS-single is available as a web server from http:\/\/single.topcons.net\/ and is also included for local installation from the web site. In addition, consensus-based topology predictions for the entire international protein index (IPI) is available from the web server and will be updated at regular intervals.<\/jats:p>\n               <jats:p>Contact: \u00a0arne@bioinfo.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are avaliable at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr119","type":"journal-article","created":{"date-parts":[[2011,4,14]],"date-time":"2011-04-14T14:46:34Z","timestamp":1302792394000},"page":"1322-1323","source":"Crossref","is-referenced-by-count":50,"title":["Rapid membrane protein topology prediction"],"prefix":"10.1093","volume":"27","author":[{"given":"Aron","family":"Hennerdal","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden"}]},{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, 106 91 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2011,4,13]]},"reference":[{"key":"2023012512184731300_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":"2023012512184731300_B2","doi-asserted-by":"crossref","first-page":"7177","DOI":"10.1073\/pnas.0711151105","article-title":"Prediction of membrane-protein topology from first principles","volume":"105","author":"Bernsel","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512184731300_B3","doi-asserted-by":"crossref","first-page":"W465","DOI":"10.1093\/nar\/gkp363","article-title":"Topcons: consensus prediction of membrane protein topology","volume":"37","author":"Bernsel","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512184731300_B4","first-page":"685","article-title":"TopPred II: an improved software for membrane protein structure predictions","volume":"10","author":"Claros","year":"1994","journal-title":"Comput. Appl. Biosci."},{"key":"2023012512184731300_B5","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1093\/bioinformatics\/14.5.423","article-title":"Removing near-neighbour redundancy from large protein sequence collections","volume":"14","author":"Holm","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012512184731300_B6","doi-asserted-by":"crossref","first-page":"3038","DOI":"10.1021\/bi00176a037","article-title":"A model recognition approach to the prediction of all-helical membrane protein structure and topology","volume":"33","author":"Jones","year":"1994","journal-title":"Biochemistry"},{"key":"2023012512184731300_B7","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1016\/j.jmb.2004.03.016","article-title":"A combined transmembrane topology and signal peptide prediction method","volume":"338","author":"K\u00e4ll","year":"2004","journal-title":"J. Mol. 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Biol."},{"key":"2023012512184731300_B10","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1093\/bioinformatics\/17.9.849","article-title":"The hmmtop transmembrane topology prediction server","volume":"17","author":"Tusn\u00e1dy","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012512184731300_B11","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1110\/ps.04625404","article-title":"Best alpha-helical transmembrane protein topology predictions are achieved using hidden markov models and evolutionary information","volume":"13","author":"Viklund","year":"2004","journal-title":"Protein Science"},{"key":"2023012512184731300_B12","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1016\/0022-2836(92)90934-C","article-title":"Membrane protein structure prediction. hydrophobicity analysis and the positive-inside rule","volume":"225","author":"von Heijne","year":"1992","journal-title":"J. Mol. 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