{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T13:59:06Z","timestamp":1775915946704,"version":"3.50.1"},"reference-count":82,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2021,6,18]],"date-time":"2021-06-18T00:00:00Z","timestamp":1623974400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["19K06532"],"award-info":[{"award-number":["19K06532"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM123055"],"award-info":[{"award-number":["R01GM123055"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM133840"],"award-info":[{"award-number":["R01GM133840"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CMMI1825941"],"award-info":[{"award-number":["CMMI1825941"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI2003635"],"award-info":[{"award-number":["DBI2003635"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS1614777"],"award-info":[{"award-number":["DMS1614777"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB1925643"],"award-info":[{"award-number":["MCB1925643"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2021,7,26]]},"DOI":"10.1021\/acs.jcim.1c00230","type":"journal-article","created":{"date-parts":[[2021,6,18]],"date-time":"2021-06-18T13:32:08Z","timestamp":1624023128000},"page":"3516-3528","source":"Crossref","is-referenced-by-count":17,"title":["Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps"],"prefix":"10.1021","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8717-2926","authenticated-orcid":true,"given":"Takaharu","family":"Mori","sequence":"first","affiliation":[{"name":"RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5339-909X","authenticated-orcid":true,"given":"Genki","family":"Terashi","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Matsuoka","sequence":"additional","affiliation":[{"name":"RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4091-6614","authenticated-orcid":true,"given":"Daisuke","family":"Kihara","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States"},{"name":"Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9738-9216","authenticated-orcid":true,"given":"Yuji","family":"Sugita","sequence":"additional","affiliation":[{"name":"RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan"},{"name":"RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan"},{"name":"RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-minamimachi,\rChuo-ku, Kobe, Hyogo 650-0047, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2021,6,18]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2019.04.008"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat4346"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.07.045"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.56862"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-020-00518-w"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1126\/science.aav8912"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1126\/science.aay3353"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2829-0"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2833-4"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1042\/BSR20170072"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2019.05.024"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.3390\/molecules25010082"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00087"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1107\/s0907444900010908"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1006\/jsbi.2000.4350"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2020.07.027"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.01.048"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2013.08.010"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.108.139451"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2008.03.005"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2007.11.016"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0101951"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2018.02.028"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2018.09.004"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.43542"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.9b01148"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3287"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2009.06.001"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2016.06.004"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04053-7"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20906"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1021\/ct500995d"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00464"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1016\/s0009-2614(99)01123-9"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.16105"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24785"},{"key":"ref37\/cit37","unstructured":"Shekhar, M.; Terashi, G.; Gupta, C.; Debussche, G.; Sisco, N. J.; Nguyen, J.; Zook, J.; Vant, J.; Sarkar, D.; Fromme, P.; Van Horn, W. D.; Dill, K.; Kihara, D.; Tajkhorshid, E.; Perez, A.; Singharoy, A. CryoFold: Ab-initio Structure Determination from Electron Density Maps Using Molecular Dynamics. 2019, bioRxiv:687087."},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1080\/08927029308022170"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1515561112"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1107\/s0907444904019158"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1107\/s2059798318006551"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1107\/s2059798318002425"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2019.12.007"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1220"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24874"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015386"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1107\/s0907444909042073"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-190"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2014.06.010"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1038\/nature16936"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1211702109"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.01299"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.07901"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2015.12.006"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.01963"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1038\/nature12822"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmgm.2003.12.005"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1063\/1.472061"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4067"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1002\/(sici)1097-0134(19990501)35:2<133::aid-prot1>3.0.co;2-n"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20033"},{"key":"ref63\/cit63","unstructured":"Schrodinger\nLLC.  The PyMOL Molecular Graphics\nSystem, version 1.8, 2015."},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360221211"},{"key":"ref65\/cit65","unstructured":"Hubbard, S.; Thornton, J. Naccess, version 2.1.1, 1993."},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1021\/ja9940524"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1038\/1368"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1111\/j.1399-3011.1975.tb02465.x"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1021\/ct400230y"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1021\/jp973371j"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1108363108"},{"key":"ref72\/cit72","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/978-1-4419-6889-0_4","volume-title":"Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies","author":"Feig M.","year":"2011"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2021.631854"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1107\/s2059798318009324"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00010"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20295-w"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3541"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-083012-130315"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbamem.2015.12.032"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.9b00783"},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23189"},{"key":"ref82\/cit82","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00254"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.1c00230","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.1c00230","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T20:22:00Z","timestamp":1682626920000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.1c00230"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,18]]},"references-count":82,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2021,7,26]]}},"alternative-id":["10.1021\/acs.jcim.1c00230"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.1c00230","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,18]]}}}