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Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology
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The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
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Biofizikai és Sugárbiológiai Intézet (SE / AOK / I); ELKH-SE Biofizikai Virológia Kutatócsoport (SE / AOK / I / BSI); Részben rendezett rendszerek csoport (SZFI / KFO)
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<div class="JournalArticle Publication short-list"> <div class="authors"> <span class="author-name" mtid="10010378"> <a href="/gui2/?type=authors&mode=browse&sel=10010378" target="_blank">Tordai, Hedvig</a> </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10084842"> <a href="/gui2/?type=authors&mode=browse&sel=10084842" target="_blank">Suhajda, Erzsebet<sup>*</sup></a> </span> <span class="author-type"> </span> ; <span class="author-name" > Sillitoe, Ian </span> <span class="author-type"> </span> ; <span class="author-name" > Nair, Sreenath </span> <span class="author-type"> </span> ; <span class="author-name" > Varadi, Mihaly </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10015687"> <a href="/gui2/?type=authors&mode=browse&sel=10015687" target="_blank">Hegedus, Tamas ✉</a> </span> <span class="author-type"> </span> </div ><div class="title"><a href="/gui2/?mode=browse¶ms=publication;33084278" mtid="33084278" target="_blank">Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology</a></div> <div class="pub-info"> <span class="journal-title">INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES</span> <span class="journal-volume">23</span> : <span class="journal-issue">16</span> <span class="page"> Paper: 8877 , 16 p. </span> <span class="year">(2022)</span> </div> <div class="pub-end"><div class="identifier-list"> <span class="identifiers"> <span class="id identifier oa_GOLD" title=" Gold "> <a style="color:blue" title="10.3390/ijms23168877" target="_blank" href="https://doi.org/10.3390/ijms23168877"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000846710500001" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000846710500001"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="85137125327" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85137125327"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="36012140" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=36012140&dopt=Abstract"> PubMed </a> </span> </span> </div> <div class="short-pub-prop-list"> <span class="short-pub-mtid"> Közlemény:33084278 </span> <span class="status-holder"><span class="status-data status-APPROVED"> Nyilvános </span></span> <span class="pub-core">Forrás Idéző </span> <span class="pub-type">Folyóiratcikk (Szakcikk ) </span> <!-- && !record.category.scientific --> <span class="pub-category">Tudományos</span> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="Nyilvános idézőközlemények összesen, említések nélkül" class="citingPub-count">Nyilvános idéző összesen: 7</span> | Független: 3 | Függő: 4 | Nem jelölt: 0 | WoS jelölt: 7 | Scopus jelölt: 6 | WoS/Scopus jelölt: 7 | DOI jelölt: 7 </div> </div> </div> </div><div class="JournalArticle Publication long-list"> <div class="authors"> <img title="Forrásközlemény" style="float: left" src="/frontend/resources/grid/publication-core-icon.png"> <img title="Idézőközlemény" style="float: left" src="/frontend/resources/grid/publication-citation-icon.png"> <div class="autype autype0"> <span class="author-name" mtid="10010378"><a href="/gui2/?type=authors&mode=browse&sel=10010378" target="_blank">Tordai Hedvig (<span class="authorship-author-name">Tordai Hedvig</span> <span class="authorAux-mtmt"> molekuláris biológia</span>) </a> </span> <span class="author-affil"><span title="Semmelweis Egyetem">SE</span>/<span title="Általános Orvostudományi Kar">AOK</span>/<span title="Intézet">I</span>/Biofizikai és Sugárbiológiai Intézet</span> ; <span class="author-name" mtid="10084842"><a href="/gui2/?type=authors&mode=browse&sel=10084842" target="_blank">Suhajda Erzsebet<sup>*</sup> (<span class="authorship-author-name">Suhajda Erzébet</span> <span class="authorAux-mtmt"> Fizika</span>) </a> </span> <span class="author-affil"><span title="Wigner Fizikai Kutatóközpont">Wigner FK</span>/<span title="Szilárdtestfizikai és Optikai Intézet">SZFI</span>/<span title="Komplex Folyadékok Osztály">KFO</span>/Részben rendezett rendszerek csoport</span> ; <span class="author-name" >Sillitoe Ian </span> ; <span class="author-name" >Nair Sreenath </span> ; <span class="author-name" >Varadi Mihaly </span> ; <span class="author-name" mtid="10015687"><a href="/gui2/?type=authors&mode=browse&sel=10015687" target="_blank">Hegedus Tamas ✉ (<span class="authorship-author-name">Hegedűs Tamás</span> <span class="authorAux-mtmt"> bioinformatika, biofizika</span>) </a> </span> <span class="author-affil"><span title="Semmelweis Egyetem">SE</span>/<span title="Általános Orvostudományi Kar">AOK</span>/<span title="Intézet">I</span>/Biofizikai és Sugárbiológiai Intézet; <span title="Semmelweis Egyetem">SE</span>/<span title="Általános Orvostudományi Kar">AOK</span>/<span title="Intézet">I</span>/<span title="Biofizikai és Sugárbiológiai Intézet">BSI</span>/ELKH-SE Biofizikai Virológia Kutatócsoport</span> </div> </div> <div class="title"><a href="/gui2/?mode=browse¶ms=publication;33084278" target="_blank">Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology</a></div> <div> <span class="journal-title">INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES</span> <span class="journal-issn">(<a target="_blank" href="https://portal.issn.org/resource/ISSN/1661-6596">1661-6596</a> <a target="_blank" href="https://portal.issn.org/resource/ISSN/1422-0067">1422-0067</a>)</span>: <span class="journal-volume">23</span> <span class="journal-issue">16</span> <span class="page"> Paper 8877. 16 p. </span> <span class="year">(2022)</span> </div> <div class="pub-footer"> <span class="language" xmlns="http://www.w3.org/1999/html">Nyelv: Angol | </span> <span class="identifiers"> <span class="id identifier oa_GOLD" title=" Gold "> <a style="color:blue" title="10.3390/ijms23168877" target="_blank" href="https://doi.org/10.3390/ijms23168877"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000846710500001" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000846710500001"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="85137125327" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85137125327"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="36012140" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=36012140&dopt=Abstract"> PubMed </a> </span> </span> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="Nyilvános idézőközlemények összesen, említések nélkül" class="citingPub-count">Nyilvános idéző összesen: 7</span> | Független: 3 | Függő: 4 | Nem jelölt: 0 | WoS jelölt: 7 | Scopus jelölt: 6 | WoS/Scopus jelölt: 7 | DOI jelölt: 7 </div> <div class="publication-citation"> <a target="_blank" href="/api/publication?cond=citations.related;eq;33084278&sort=publishedYear,desc&sort=title"> Idézett közlemények száma: 16 </a> </div> <div class="mtid"><span class="long-pub-mtid">Közlemény: 33084278</span> | <span class="status-data status-APPROVED"> Nyilvános </span> Forrás Idéző | <span class="type-subtype">Folyóiratcikk ( Szakcikk ) </span> | <span class="pub-category">Tudományos</span> | <span class="publication-sourceOfData">WOS TAGGED</span> </div> <div class="funder"> (K127961) Támogató: NKFIH, (K137610), (2020-2.1.1-ED-2021-00179), (HEGEDU20I0) </div> <div class="lastModified">Utolsó módosítás: 2024.02.07. 03:01 Kmety Andrea (MTA Wigner, admin) </div> </div></div>