{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T21:08:25Z","timestamp":1790456905203,"version":"4.1.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1242,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt385","type":"journal-article","created":{"date-parts":[[2013,5,14]],"date-time":"2013-05-14T03:27:06Z","timestamp":1368502026000},"page":"W363-W367","source":"Crossref","is-referenced-by-count":15,"title":["3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy"],"prefix":"10.1093","volume":"41","author":[{"given":"R.","family":"Nogales-Cadenas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Jonic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F.","family":"Tama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. A.","family":"Arteni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Tabas-Madrid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"V\u00e1zquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Pascual-Montano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. O. S.","family":"Sorzano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,5,11]]},"reference":[{"key":"key\n\t\t\t\t20171013170738_gkt385-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/protein\/14.1.1","article-title":"Conformational change of proteins arising from normal mode calculations","volume":"14","author":"Tama","year":"2001","journal-title":"Protein Eng."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B2","doi-asserted-by":"crossref","first-page":"119","DOI":"10.2174\/0929866033479077","article-title":"Normal mode analysis with simplified models to investigate the global dynamics of biological systems","volume":"10","author":"Tama","year":"2003","journal-title":"Protein Pept. Lett."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B3","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/S0022-2836(02)00627-7","article-title":"Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory","volume":"321","author":"Tama","year":"2002","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B4","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/S0022-2836(02)01426-2","article-title":"Mega-dalton biomolecular motion captured from electron microscopy reconstructions","volume":"326","author":"Chac\u00f3n","year":"2003","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B5","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.jsb.2004.03.002","article-title":"Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM","volume":"147","author":"Tama","year":"2004","journal-title":"J. Struct. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B6","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1016\/j.jmb.2004.01.048","article-title":"Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis","volume":"337","author":"Tama","year":"2004","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B7","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1107\/S090744490602244X","article-title":"NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps","volume":"62","author":"Suhre","year":"2006","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B8","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.jsb.2010.09.015","article-title":"Conformational dynamics of supramolecular protein assemblies","volume":"173","author":"Kim","year":"2011","journal-title":"J. Struct. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B9","doi-asserted-by":"crossref","first-page":"W610","DOI":"10.1093\/nar\/gkh368","article-title":"ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement","volume":"32","author":"Suhre","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B10","doi-asserted-by":"crossref","first-page":"13253","DOI":"10.1073\/pnas.2235686100","article-title":"A comparative study of motor-protein motions by using a simple elastic-network model","volume":"100","author":"Zheng","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013170738_gkt385-B11","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/1471-2105-6-52","article-title":"WEBnm@: a web application for normal mode analyses of proteins","volume":"6","author":"Hollup","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013170738_gkt385-B12","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1002\/1097-0134(20000815)40:3<512::AID-PROT180>3.0.CO;2-M","article-title":"Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor","volume":"40","author":"Doruker","year":"2000","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013170738_gkt385-B13","doi-asserted-by":"crossref","first-page":"W52","DOI":"10.1093\/nar\/gkl082","article-title":"NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis","volume":"34","author":"Lindahl","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B14","doi-asserted-by":"crossref","first-page":"D451","DOI":"10.1093\/nar\/gkq1088","article-title":"Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies","volume":"39","author":"Kim","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B15","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1006\/jmbi.1998.2232","article-title":"Self-organizing neural networks bridge the biomolecular resolution gap","volume":"284","author":"Wriggers","year":"1998","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B16","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.jsb.2006.08.008","article-title":"Multi-resolution anchor-point registration of biomolecular assemblies and their components","volume":"157","author":"Birmanns","year":"2007","journal-title":"J. Struct. Biol."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B17","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1103\/PhysRevLett.77.1905","article-title":"Large amplitude elastic motions in proteins from a single-parameter, atomic analysis","volume":"77","author":"Tirion","year":"1996","journal-title":"Phys. Rev. Lett."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B18","doi-asserted-by":"crossref","first-page":"3396","DOI":"10.1063\/1.469213","article-title":"Collective protein dynamics and nuclear spin relaxation","volume":"102","author":"Br\u00fcschweiler","year":"1995","journal-title":"J. Chem. Phys."},{"key":"key\n\t\t\t\t20171013170738_gkt385-B19","doi-asserted-by":"crossref","first-page":"6031","DOI":"10.1021\/bi00238a029","article-title":"Crystal structure of an open conformation of citrate synthase from chicken heart at 2.8-.ANG resolution","volume":"30","author":"Liao","year":"1991","journal-title":"Biochemistry"},{"key":"key\n\t\t\t\t20171013170738_gkt385-B20","doi-asserted-by":"crossref","first-page":"6024","DOI":"10.1021\/bi00238a028","article-title":"1.9-.ANG. Structures of ternary complexes of citrate synthase with D- and L-malate: mechanistic implications","volume":"30","author":"Karpusas","year":"1991","journal-title":"Biochemistry"},{"key":"key\n\t\t\t\t20171013170738_gkt385-B21","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.jsb.2004.06.006","article-title":"XMIPP: a new generation of an open-source image processing package for electron microscopy","volume":"148","author":"Sorzano","year":"2004","journal-title":"J. Struct. Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W363\/3836284\/gkt385.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:41:17Z","timestamp":1522680077000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W363\/1098208\/3DEM-Loupe-analysis-of-macromolecular-dynamics"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,11]]},"references-count":21,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,5,11]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt385","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,5,11]]}}}