{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:10Z","timestamp":1740185110877,"version":"3.37.3"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,7,10]],"date-time":"2019-07-10T00:00:00Z","timestamp":1562716800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Research, Development and Innovation Office","award":["K111678","K119287","K125607","K127961"],"award-info":[{"award-number":["K111678","K119287","K125607","K127961"]}]},{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["CFF HEGEDU18I0"],"award-info":[{"award-number":["CFF HEGEDU18I0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Semmelweis Science and Innovation Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The identification of transmembrane helices in transmembrane proteins is crucial, not only to understand their mechanism of action but also to develop new therapies. While experimental data on the boundaries of membrane-embedded regions are sparse, this information is present in cryo-electron microscopy (cryo-EM) density maps and it has not been utilized yet for determining membrane regions. We developed a computational pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientation determined by TMDET algorithm of a given protein result in an output defining the residues assigned to the bulk water phase, lipid interface and the lipid hydrophobic core. Based on this method, we built a database involving published cryo-EM protein structures and a server to be able to compute this data for newly obtained structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/memblob.hegelab.org.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz539","type":"journal-article","created":{"date-parts":[[2019,7,9]],"date-time":"2019-07-09T11:11:18Z","timestamp":1562670678000},"page":"2595-2598","source":"Crossref","is-referenced-by-count":6,"title":["MemBlob database and server for identifying transmembrane regions using cryo-EM maps"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0258-6864","authenticated-orcid":false,"given":"Bianka","family":"Farkas","sequence":"first","affiliation":[{"name":"Department of Biophysics and Radiation Biology, Semmelweis University , Budapest 1094, Hungary"},{"name":"MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences , Budapest 1094, Hungary"},{"name":"Faculty of Information Technology and Bionics, P\u00e1zm\u00e1ny P\u00e9ter Catholic University , Budapest 1083, Hungary"}]},{"given":"Georgina","family":"Csizmadia","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Radiation Biology, Semmelweis University , Budapest 1094, Hungary"},{"name":"MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences , Budapest 1094, Hungary"}]},{"given":"Eszter","family":"Katona","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Radiation Biology, Semmelweis University , Budapest 1094, Hungary"},{"name":"Faculty of Brain Sciences, University College London , London W1T 7NF, UK"}]},{"given":"G\u00e1bor E","family":"Tusn\u00e1dy","sequence":"additional","affiliation":[{"name":"\u2018Momentum\u2019 Membrane Protein Bioinformatics Research Group, Institute of Enzymology , RCNS, Hungarian Academy of Sciences, 1117 Budapest, Hungary"}]},{"given":"Tam\u00e1s","family":"Heged\u0171s","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Radiation Biology, Semmelweis University , Budapest 1094, Hungary"},{"name":"MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences , Budapest 1094, Hungary"}]}],"member":"286","published-online":{"date-parts":[[2019,7,10]]},"reference":[{"key":"2023013110262050400_btz539-B1","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":"2023013110262050400_btz539-B2","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1085\/jgp.201110766","article-title":"Membrane bending is critical for the stability of voltage sensor segments in the membrane","volume":"140","author":"Callenberg","year":"2012","journal-title":"J. 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