{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T09:13:55Z","timestamp":1720602835691},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: ExTopoDB is a publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains information collected from studies in the literature that report the use of biochemical methods for the determination of the topology of \u03b1-helical transmembrane proteins. Transmembrane protein topology is highly important in order to understand their function and ExTopoDB provides an up to date, complete and comprehensive dataset of experimentally determined topologies of \u03b1-helical transmembrane proteins. Topological information is combined with transmembrane topology prediction resulting in more reliable topological models.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioinformatics.biol.uoa.gr\/ExTopoDB<\/jats:p>\n               <jats:p>Contact: \u00a0shamodr@biol.uoa.gr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq362","type":"journal-article","created":{"date-parts":[[2010,7,4]],"date-time":"2010-07-04T00:26:27Z","timestamp":1278203187000},"page":"2490-2492","source":"Crossref","is-referenced-by-count":16,"title":["ExTopoDB: a database of experimentally derived topological models of transmembrane proteins"],"prefix":"10.1093","volume":"26","author":[{"given":"Georgios N.","family":"Tsaousis","sequence":"first","affiliation":[{"name":"1 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis Athens 15701 and 2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4 Lamia 35100, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Konstantinos D.","family":"Tsirigos","sequence":"additional","affiliation":[{"name":"1 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis Athens 15701 and 2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4 Lamia 35100, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xanthi D.","family":"Andrianou","sequence":"additional","affiliation":[{"name":"1 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis Athens 15701 and 2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4 Lamia 35100, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Theodore D.","family":"Liakopoulos","sequence":"additional","affiliation":[{"name":"1 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis Athens 15701 and 2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4 Lamia 35100, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pantelis G.","family":"Bagos","sequence":"additional","affiliation":[{"name":"1 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis Athens 15701 and 2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4 Lamia 35100, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stavros J.","family":"Hamodrakas","sequence":"additional","affiliation":[{"name":"1 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis Athens 15701 and 2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4 Lamia 35100, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,7,3]]},"reference":[{"key":"2023012508171125000_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":"2023012508171125000_B2","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/1471-2105-7-189","article-title":"Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins","volume":"7","author":"Bagos","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012508171125000_B3","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The Universal Protein Resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012508171125000_B4","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","article-title":"Assessing the accuracy of prediction algorithms for classification: an overview","volume":"16","author":"Baldi","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012508171125000_B5","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.jmb.2004.05.028","article-title":"Improved prediction of signal peptides: SignalP 3.0","volume":"340","author":"Bendtsen","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012508171125000_B6","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012508171125000_B7","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":"2023012508171125000_B8","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1109730","article-title":"Global topology analysis of the Escherichia coli inner membrane proteome","volume":"308","author":"Daley","year":"2005","journal-title":"Science"},{"key":"2023012508171125000_B9","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nature06387","article-title":"Molecular code for transmembrane-helix recognition by the Sec61 translocon","volume":"450","author":"Hessa","year":"2007","journal-title":"Nature"},{"key":"2023012508171125000_B10","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1093\/nar\/gkg020","article-title":"TMPDB: a database of experimentally-characterized transmembrane topologies","volume":"31","author":"Ikeda","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012508171125000_B11","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1110\/ps.43501","article-title":"MPtopo: A database of membrane protein topology","volume":"10","author":"Jayasinghe","year":"2001","journal-title":"Protein Sci."},{"key":"2023012508171125000_B12","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":"Kall","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012508171125000_B13","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012508171125000_B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0005-2736(03)00056-7","article-title":"Lipid-protein interactions in biological membranes: a structural perspective","volume":"1612","author":"Lee","year":"2003","journal-title":"Biochim. Biophys. Acta"},{"key":"2023012508171125000_B15","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1093\/bioinformatics\/btk023","article-title":"OPM: orientations of proteins in membranes database","volume":"22","author":"Lomize","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508171125000_B16","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1016\/S0022-2836(03)00182-7","article-title":"Reliability measures for membrane protein topology prediction algorithms","volume":"327","author":"Melen","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2023012508171125000_B17","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1093\/bioinformatics\/16.12.1159","article-title":"A collection of well characterised integral membrane proteins","volume":"16","author":"Moller","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012508171125000_B18","doi-asserted-by":"crossref","first-page":"2974","DOI":"10.1110\/ps.0226702","article-title":"Prediction of partial membrane protein topologies using a consensus approach","volume":"11","author":"Nilsson","year":"2002","journal-title":"Protein Sci."},{"key":"2023012508171125000_B19","doi-asserted-by":"crossref","first-page":"14037","DOI":"10.1073\/pnas.182552199","article-title":"An approach to membrane protein structure without crystals","volume":"99","author":"Sorgen","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508171125000_B20","doi-asserted-by":"crossref","first-page":"D275","DOI":"10.1093\/nar\/gki002","article-title":"PDB\n            \u00a0TM: selection and membrane localization of transmembrane proteins in the protein data bank","volume":"33","author":"Tusnady","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012508171125000_B21","doi-asserted-by":"crossref","first-page":"D234","DOI":"10.1093\/nar\/gkm751","article-title":"TOPDB: topology data bank of transmembrane proteins","volume":"36","author":"Tusnady","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012508171125000_B22","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":"Tusnady","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012508171125000_B23","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1128\/MMBR.64.1.13-33.2000","article-title":"Membrane topology and insertion of membrane proteins: search for topogenic signals","volume":"64","author":"van Geest","year":"2000","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"2023012508171125000_B24","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1002\/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K","article-title":"A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment","volume":"34","author":"Zemla","year":"1999","journal-title":"Proteins"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/19\/2490\/48856285\/bioinformatics_26_19_2490.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/19\/2490\/48856285\/bioinformatics_26_19_2490.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:18:15Z","timestamp":1674634695000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/19\/2490\/228646"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7,3]]},"references-count":24,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2010,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq362","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,10,1]]},"published":{"date-parts":[[2010,7,3]]}}}