{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T05:53:05Z","timestamp":1784872385762,"version":"3.55.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T00:00:00Z","timestamp":1711065600000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Science and Technology Major Project of China","award":["2022ZD0115103"],"award-info":[{"award-number":["2022ZD0115103"]}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["62203389"],"award-info":[{"award-number":["62203389"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["62201506"],"award-info":[{"award-number":["62201506"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI1548562"],"award-info":[{"award-number":["ACI1548562"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The breakthrough in cryo-electron microscopy (cryo-EM) technology has led to an increasing number of density maps of biological macromolecules. However, constructing accurate protein complex atomic structures from cryo-EM maps remains a challenge. In this study, we extend our previously developed DEMO-EM to present DEMO-EM2, an automated method for constructing protein complex models from cryo-EM maps through an iterative assembly procedure intertwining chain- and domain-level matching and fitting for predicted chain models. The method was carefully evaluated on 27 cryo-electron tomography (cryo-ET) maps and 16 single-particle EM maps, where DEMO-EM2 models achieved an average TM-score of 0.92, outperforming those of state-of-the-art methods. The results demonstrate an efficient method that enables the rapid and reliable solution of challenging cryo-EM structure modeling problems.<\/jats:p>","DOI":"10.1093\/bib\/bbae113","type":"journal-article","created":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T14:15:54Z","timestamp":1711116954000},"source":"Crossref","is-referenced-by-count":26,"title":["DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting"],"prefix":"10.1093","volume":"25","author":[{"given":"Ziying","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaxian","family":"Cai","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Biao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2984-9003","authenticated-orcid":false,"given":"Wei","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5821-4226","authenticated-orcid":false,"given":"Lydia","family":"Freddolino","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7815-5884","authenticated-orcid":false,"given":"Guijun","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6839-1923","authenticated-orcid":false,"given":"Xiaogen","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,3,19]]},"reference":[{"key":"2024032214145287400_ref1","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/s41586-020-2833-4","article-title":"Atomic-resolution protein structure determination by cryo-EM","volume":"587","author":"Yip","year":"2020","journal-title":"Nature"},{"key":"2024032214145287400_ref2","doi-asserted-by":"crossref","first-page":"D396","DOI":"10.1093\/nar\/gkv1126","article-title":"EMDataBank unified data resource for 3DEM","volume":"44","author":"Lawson","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024032214145287400_ref3","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1107\/S0907444906022116","article-title":"The Buccaneer software for automated model building. 1. 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