{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T18:45:16Z","timestamp":1776019516067,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,6]],"date-time":"2017-11-06T00:00:00Z","timestamp":1509926400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000153","name":"Division of Biological Infrastructure","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000153","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["#1145367 and # 1458002"],"award-info":[{"award-number":["#1145367 and # 1458002"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Structural studies of TM domains of single-spanning (bitopic) membrane proteins are impeded by their instability, flexibility and heterogeneity. The new computational method TMDOCK allows reliable modeling of homodimers of transmembrane (TM) \u03b1-helices on a proteomic scale.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n 3D models of 2129 parallel homodimers formed by TM \u03b1-helices of bitopic proteins from six evolutionarily distant organisms were modeled by TMDOCK, verified through experimental data available for nearly 600 proteins, and included in the Membranome database (v.2.0) along with related information to facilitate structural and evolutionary analysis of bitopic proteins.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n http:\/\/membranome.org<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx720","type":"journal-article","created":{"date-parts":[[2017,11,4]],"date-time":"2017-11-04T12:08:59Z","timestamp":1509797339000},"page":"1061-1062","source":"Crossref","is-referenced-by-count":36,"title":["Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers"],"prefix":"10.1093","volume":"34","author":[{"given":"Andrei L","family":"Lomize","sequence":"first","affiliation":[{"name":"Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Jacob M","family":"Hage","sequence":"additional","affiliation":[{"name":"Electrical Engineering and Computer Science Department, College of Engineering, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Irina D","family":"Pogozheva","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,11,6]]},"reference":[{"key":"2023012712464227900_btx720-B1","doi-asserted-by":"crossref","first-page":"313","DOI":"10.4161\/cam.4.2.12430","article-title":"Single-spanning transmembrane domains in cell growth and cell-cell interactions: more than meets the eye?","volume":"4","author":"Hubert","year":"2010","journal-title":"Cell Adhes. Migr"},{"key":"2023012712464227900_btx720-B2","doi-asserted-by":"crossref","first-page":"D250","DOI":"10.1093\/nar\/gkw712","article-title":"Membranome: a database for proteome-wide analysis of single-pass membrane proteins","volume":"45","author":"Lomize","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012712464227900_btx720-B3","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.jmb.2016.09.005","article-title":"TMDOCK: an energy-based method for modeling alpha-helical dimers in membranes","volume":"429","author":"Lomize","year":"2017","journal-title":"J. Mol. Biol"},{"key":"2023012712464227900_btx720-B4","doi-asserted-by":"crossref","first-page":"E888","DOI":"10.1073\/pnas.1319944111","article-title":"A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Calpha-H hydrogen bonds","volume":"111","author":"Mueller","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712464227900_btx720-B5","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btt645","article-title":"PREDDIMER: a web server for prediction of transmembrane helical dimers","volume":"30","author":"Polyansky","year":"2014","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1061\/48913531\/bioinformatics_34_6_1061.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1061\/48913531\/bioinformatics_34_6_1061.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:48:53Z","timestamp":1674823733000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/6\/1061\/4596946"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,6]]},"references-count":5,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx720","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,3,15]]},"published":{"date-parts":[[2017,11,6]]}}}