{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T19:27:59Z","timestamp":1791833279208,"version":"4.3.4"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020"},{"DOI":"10.13039\/501100012550","name":"National Research, Development and Innovation Fund","doi-asserted-by":"publisher","award":["K132522"],"award-info":[{"award-number":["K132522"]}],"id":[{"id":"10.13039\/501100012550","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional structure prediction methods for transmembrane proteins were both complicated and error prone, AF2 is a great help to the community. Complementing the relatively meager number of experimental structures, AF2 provides 3D\u00a0predictions for thousands of new alpha-helical membrane proteins. However, the lack of reliable structural templates and the fact that AF2 was not trained to handle phase boundaries also necessitates a delicate assessment of structural correctness. In our new database, Transmembrane AlphaFold database (TmAlphaFold database), we apply TMDET, a simple geometry-based method to visualize the likeliest position of the membrane plane. In addition, we calculate several parameters to evaluate the location of the protein into the membrane. This also allows TmAlphaFold database to show whether the predicted 3D structure is realistic or not. The TmAlphaFold database is available at https:\/\/tmalphafold.ttk.hu\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac928","type":"journal-article","created":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T16:43:40Z","timestamp":1665161020000},"page":"D517-D522","source":"Crossref","is-referenced-by-count":97,"title":["TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures"],"prefix":"10.1093","volume":"51","author":[{"given":"Laszlo","family":"Dobson","sequence":"first","affiliation":[{"name":"Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences , Magyar Tud\u00f3sok k\u00f6r\u00fatja 2, H-1117\u00a0 Budapest ,\u00a0 Hungary"},{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , Meyerhofstra\u00dfe 1, 69117\u00a0 Heidelberg ,\u00a0 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levente I","family":"Szekeres","sequence":"additional","affiliation":[{"name":"Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences , Magyar Tud\u00f3sok k\u00f6r\u00fatja 2, H-1117\u00a0 Budapest ,\u00a0 Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Csongor","family":"Gerd\u00e1n","sequence":"additional","affiliation":[{"name":"Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences , Magyar Tud\u00f3sok k\u00f6r\u00fatja 2, H-1117\u00a0 Budapest ,\u00a0 Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tam\u00e1s","family":"Lang\u00f3","sequence":"additional","affiliation":[{"name":"Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences , Magyar Tud\u00f3sok k\u00f6r\u00fatja 2, H-1117\u00a0 Budapest ,\u00a0 Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e1s","family":"Zeke","sequence":"additional","affiliation":[{"name":"Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences , Magyar Tud\u00f3sok k\u00f6r\u00fatja 2, H-1117\u00a0 Budapest ,\u00a0 Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8105-0285","authenticated-orcid":false,"given":"G\u00e1bor E","family":"Tusn\u00e1dy","sequence":"additional","affiliation":[{"name":"Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences , Magyar Tud\u00f3sok k\u00f6r\u00fatja 2, H-1117\u00a0 Budapest ,\u00a0 Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"2023010804331055600_B1","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023010804331055600_B2","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/S0014-5793(02)03730-4","article-title":"Reliability of transmembrane predictions in whole-genome data","volume":"532","author":"K\u00e4ll","year":"2002","journal-title":"FEBS Lett."},{"key":"2023010804331055600_B3","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s13062-015-0061-x","article-title":"The human transmembrane proteome","volume":"10","author":"Dobson","year":"2015","journal-title":"Biol. 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