{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T14:09:48Z","timestamp":1783433388116,"version":"3.54.6"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The structure of integral membrane proteins is determined in the absence of the lipid bilayer; consequently the membrane localization of the protein is usually not specified in the corresponding PDB file. Recently, we have developed a new method called TMDET which determines the most possible localization of the membrane relative to the protein structure, and gives the annotation of the membrane embedded parts of the sequence. The entire Protein Data Bank has been scanned by the new TMDET algorithm resulting in the database of structurally determined transmembrane proteins (PDB_TM). Here we present the web interface of the TMDET algorithm to allow scientists to determine the membrane localization of structural data prior to deposition or to analyze model structures.<\/jats:p>\n               <jats:p>Availability: The TMDET server is available for academic users on http:\/\/www.enzim.hu\/TMDET<\/jats:p>\n               <jats:p>Contact: \u00a0tusi@enzim.hu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti121","type":"journal-article","created":{"date-parts":[[2004,11,12]],"date-time":"2004-11-12T01:14:59Z","timestamp":1100222099000},"page":"1276-1277","source":"Crossref","is-referenced-by-count":133,"title":["TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates"],"prefix":"10.1093","volume":"21","author":[{"given":"G\u00e1bor E.","family":"Tusn\u00e1dy","sequence":"first","affiliation":[{"name":"Institute of Enzymology, BRC, Hungarian Academy of Sciences H-1518 Budapest, PO Box 7, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zsuzsanna","family":"Doszt\u00e1nyi","sequence":"additional","affiliation":[{"name":"Institute of Enzymology, BRC, Hungarian Academy of Sciences H-1518 Budapest, PO Box 7, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Istv\u00e1n","family":"Simon","sequence":"additional","affiliation":[{"name":"Institute of Enzymology, BRC, Hungarian Academy of Sciences H-1518 Budapest, PO Box 7, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2004,11,11]]},"reference":[{"key":"2023013107420081100_B1","unstructured":"Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E. 2000The Protein Data Bank. Nucleic Acids Res.28235\u2013242"},{"key":"2023013107420081100_B2","unstructured":"DeLano, W.L. The PyMOL Molecular Graphich System2003, CA, USA  http:\/\/pymol.sourceforge.net DeLano Scientific LLC San Carlos"},{"key":"2023013107420081100_B3","doi-asserted-by":"crossref","unstructured":"Kabsch, W. and Sander, C. 1983Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers22,  pp. 2577\u20132637","DOI":"10.1002\/bip.360221211"},{"key":"2023013107420081100_B4","unstructured":"Lee, A.G. 2003Lipid-protein interactions in biological membranes: A structural perspective. Biochim. Biophys. Acta16121\u201340"},{"key":"2023013107420081100_B5","unstructured":"Lee, B. and Richards, F.M. 1971The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol.55379\u2013400"},{"key":"2023013107420081100_B6","unstructured":"Ostermeier, C. and Michel, H. 1997Crystallization of membrane proteins. Curr. Opin. Struct. Biol.7697\u2013701"},{"key":"2023013107420081100_B7","unstructured":"Tusn\u00e1dy, G.E., Doszt\u00e1nyi, Zs., Simon, I. 2004Transmembrane proteins in Protein Data Bank: identification and classification. Bioinformatics202964\u20132972"},{"key":"2023013107420081100_B8","doi-asserted-by":"crossref","unstructured":"Tusn\u00e1dy, G.E., Doszt\u00e1nyi, Zs., Simon, I. 2005PDB_TM: selection and membrane localization of transmembrane proteins in the Protein Data Bank. Nucleic Acids Res.33D275\u2013D278","DOI":"10.1093\/nar\/gki002"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/7\/1276\/48972356\/bioinformatics_21_7_1276.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/7\/1276\/48972356\/bioinformatics_21_7_1276.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:19:29Z","timestamp":1675160369000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/7\/1276\/268950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,11,11]]},"references-count":8,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2005,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti121","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,4,1]]},"published":{"date-parts":[[2004,11,11]]}}}