{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T01:02:49Z","timestamp":1784941369394,"version":"3.55.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2017,5,12]],"date-time":"2017-05-12T00:00:00Z","timestamp":1494547200000},"content-version":"vor","delay-in-days":2079,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1]]},"DOI":"10.1093\/nar\/gkr703","type":"journal-article","created":{"date-parts":[[2011,9,4]],"date-time":"2011-09-04T00:33:59Z","timestamp":1315096439000},"page":"D370-D376","source":"Crossref","is-referenced-by-count":2151,"title":["OPM database and PPM web server: resources for positioning of proteins in membranes"],"prefix":"10.1093","volume":"40","author":[{"given":"Mikhail A.","family":"Lomize","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irina D.","family":"Pogozheva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyeon","family":"Joo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henry I.","family":"Mosberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrei L.","family":"Lomize","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,9,2]]},"reference":[{"key":"key\n\t\t\t\t20170512131345_gkr703-B1","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1002\/pro.5560070420","article-title":"Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms","volume":"7","author":"Wallin","year":"1998","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B2","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nbt.1833","article-title":"Overcoming barriers to membrane protein structure determination","volume":"29","author":"Bill","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B3","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"Berman","year":"2002","journal-title":"Acta Crystallogr. D"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B4"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B5","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1007\/s00018-005-5350-6","article-title":"The membrane protein data bank","volume":"63","author":"Raman","year":"2006","journal-title":"Cell. Mol. Life Sci."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B6","doi-asserted-by":"crossref","first-page":"D274","DOI":"10.1093\/nar\/gkn862","article-title":"The transporter classification database: recent advances","volume":"37","author":"Saier","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B7","doi-asserted-by":"crossref","first-page":"3110","DOI":"10.1093\/bioinformatics\/btm395","article-title":"MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins","volume":"23","author":"Bhardwaj","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B8","doi-asserted-by":"crossref","first-page":"D593","DOI":"10.1093\/nar\/gkh077","article-title":"The peptaibol database: a database for sequences and structures of naturally occurring peptaibols","volume":"32","author":"Whitmore","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B9","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1110\/ps.062126106","article-title":"Positioning of proteins in membranes: a computational approach","volume":"15","author":"Lomize","year":"2006","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B10","first-page":"7","article-title":"The role of hydrophobic interactions in positioning of peripheral proteins in membranes","author":"Lomize","year":"2007","journal-title":"BMC Struct. Biol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B11","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.sbi.2005.07.007","article-title":"Molecular dynamics simulations of proteins in lipid bilayers","volume":"15","author":"Gumbart","year":"2005","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B12","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1042\/BST0360027","article-title":"Coarse-grained simulation: a high-throughput computational approach to membrane proteins","volume":"36","author":"Sansom","year":"2008","journal-title":"Biochem. Soc. T."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B13","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1016\/S0006-3495(97)78203-1","article-title":"Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles","volume":"73","author":"BenTal","year":"1997","journal-title":"Biophys. J."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B14","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1016\/S0969-2126(97)00251-7","article-title":"Electrostatic interaction of myristoylated proteins with membranes: simple physics, complicated biology","volume":"5","author":"Murray","year":"1997","journal-title":"Structure"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B15","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S1097-2765(01)00426-9","article-title":"Electrostatic control of the membrane targeting of C2 domains","volume":"9","author":"Murray","year":"2002","journal-title":"Mol. Cell"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B16","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nmeth0208-119","article-title":"MAPAS: a tool for predicting membrane-contacting protein surfaces","volume":"5","author":"Sharikov","year":"2008","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B17","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.sbi.2004.03.009","article-title":"Recent advances in the development and application of implicit solvent models in biomolecule simulations","volume":"14","author":"Feig","year":"2004","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B18","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1002\/(SICI)1097-0134(19980301)30:4<357::AID-PROT3>3.0.CO;2-G","article-title":"IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies","volume":"30","author":"Ducarme","year":"1998","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B19","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1002\/prot.20358","article-title":"Implicit solvent simulations of peptide interactions with anionic lipid membranes","volume":"58","author":"Lazaridis","year":"2005","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B20","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.2174\/0929867043364496","article-title":"Peptides and proteins in membranes: what can we learn via computer simulations?","volume":"11","author":"Efremov","year":"2004","journal-title":"Curr. Med. Chem."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B21","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1002\/prot.10410","article-title":"Effective energy function for proteins in lipid membranes","volume":"52","author":"Lazaridis","year":"2003","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B22","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1016\/j.jmb.2006.09.020","article-title":"E-z, a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: Derivation and applications to determining the orientation of transmembrane and interfacial helices","volume":"366","author":"Senes","year":"2007","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B23","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1093\/bioinformatics\/bti121","article-title":"TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates","volume":"21","author":"Tusnady","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B24","first-page":"106","article-title":"MAPS: An interactive web server for membrane annotation of transmembrane protein structures","volume":"48","author":"Cheema","year":"2011","journal-title":"Ind. J. Biochem. Biophys."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B25","doi-asserted-by":"crossref","first-page":"D275","DOI":"10.1093\/nar\/gki002","article-title":"PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank","volume":"33","author":"Tusnady","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B26","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1080\/09687680802446534","article-title":"CGDB: A database of membrane protein\/lipid interactions by coarse-grained molecular dynamics simulations","volume":"25","author":"Chetwynd","year":"2008","journal-title":"Mol. Membr. Biol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B27","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1021\/ci200020k","article-title":"Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes","volume":"51","author":"Lomize","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B28","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1093\/bioinformatics\/btk023","article-title":"OPM: Orientations of proteins in membranes database","volume":"22","author":"Lomize","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B29","doi-asserted-by":"crossref","first-page":"D308","DOI":"10.1093\/nar\/gkp916","article-title":"PDBe: Protein Data Bank in Europe","volume":"38","author":"Velankar","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B30","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.jmb.2007.05.022","article-title":"Inference of macromolecular assemblies from crystalline state","volume":"372","author":"Krissinel","year":"2007","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B31","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkp846","article-title":"The Universal Protein Resource (UniProt) in 2010","volume":"38","author":"Consortium","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B32","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1093\/nar\/30.1.276","article-title":"The Pfam Protein Families Database","volume":"30","author":"Bateman","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B33","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gkm993","article-title":"Data growth and its impact on the SCOP database: new developments","volume":"36","author":"Andreeva","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B34","doi-asserted-by":"crossref","first-page":"2356","DOI":"10.1529\/biophysj.108.132662","article-title":"Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data","volume":"95","author":"Kucerka","year":"2008","journal-title":"Biophys. J."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B35","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1007\/s00249-002-0245-z","article-title":"Membrane water-penetration profiles from spin labels","volume":"31","author":"Marsh","year":"2002","journal-title":"Eur.Biophys. J. Biophy."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B36"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B37","article-title":"Jmol: an open-source Java viewer for chemical structures in 3D"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B38","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/S0968-0004(97)89047-0","article-title":"WebMol - A Java-based PDB viewer","volume":"22","author":"Walther","year":"1997","journal-title":"Trends Biochem. Sci."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B39","doi-asserted-by":"crossref","first-page":"D266","DOI":"10.1093\/nar\/gki001","article-title":"PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids","volume":"33","author":"Laskowski","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B40","article-title":"OCA, a browser-database for protein structure\/function","author":"Prilusky","year":"1996"},{"key":"key\n\t\t\t\t20170512131345_gkr703-B41","doi-asserted-by":"crossref","first-page":"D298","DOI":"10.1093\/nar\/gkl952","article-title":"MMDB: annotating protein sequences with Entrez's 3D-structure database","volume":"35","author":"Wang","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B42","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.bpj.2009.04.013","article-title":"CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes","volume":"97","author":"Jo","year":"2009","journal-title":"Biophys. J."},{"key":"key\n\t\t\t\t20170512131345_gkr703-B43","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1021\/ci1003619","article-title":"CELLmicrocosmos 2.2 membrane editor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems","volume":"51","author":"Sommer","year":"2011","journal-title":"J. Chem. Inf. Model."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","deposited":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T22:35:30Z","timestamp":1560551730000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkr703"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,9,2]]},"references-count":43,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2011,9,2]]},"published-print":{"date-parts":[[2012,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkr703","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published":{"date-parts":[[2011,9,2]]}}}