{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T16:45:54Z","timestamp":1775666754268,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,5,23]],"date-time":"2022-05-23T00:00:00Z","timestamp":1653264000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P30 DA035778A1"],"award-info":[{"award-number":["P30 DA035778A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01DA052329"],"award-info":[{"award-number":["R01DA052329"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Antibodies are essential to life, and knowing their structures can facilitate the understanding of antibody\u2013antigen recognition mechanisms. Precise antibody structure prediction has been a core challenge for a prolonged period, especially the accuracy of H3 loop prediction. Despite recent progress, existing methods cannot achieve atomic accuracy, especially when the homologous structures required for these methods are not available. Recently, RoseTTAFold, a deep learning-based algorithm, has shown remarkable breakthroughs in predicting the 3D structures of proteins. To assess the antibody modeling ability of RoseTTAFold, we first retrieved the sequences of 30 antibodies as the test set and used RoseTTAFold to model their 3D structures. We then compared the models constructed by RoseTTAFold with those of SWISS-MODEL in a different way, in which we stratified Global Model Quality Estimate (GMQE) into three different ranges. The results indicated that RoseTTAFold could achieve results similar to SWISS-MODEL in modeling most CDR loops, especially the templates with a GMQE score under 0.8. In addition, we also compared the structures modeled by RoseTTAFold, SWISS-MODEL and ABodyBuilder. In brief, RoseTTAFold could accurately predict 3D structures of antibodies, but its accuracy was not as good as the other two methods. However, RoseTTAFold exhibited better accuracy for modeling H3 loop than ABodyBuilder and was comparable to SWISS-MODEL. Finally, we discussed the limitations and potential improvements of the current RoseTTAFold, which may help to further the accuracy of RoseTTAFold\u2019s antibody modeling.<\/jats:p>","DOI":"10.1093\/bib\/bbac152","type":"journal-article","created":{"date-parts":[[2022,5,2]],"date-time":"2022-05-02T19:10:53Z","timestamp":1651518653000},"source":"Crossref","is-referenced-by-count":40,"title":["Differential performance of RoseTTAFold in antibody modeling"],"prefix":"10.1093","volume":"23","author":[{"given":"Tianjian","family":"Liang","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261 , USA"}]},{"given":"Chen","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261 , USA"}]},{"given":"Jiayi","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261 , USA"}]},{"given":"Yasmin","family":"Othman","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261 , USA"}]},{"given":"Xiang-Qun","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6533-8932","authenticated-orcid":false,"given":"Zhiwei","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261 , USA"}]}],"member":"286","published-online":{"date-parts":[[2022,5,23]]},"reference":[{"key":"2022092013193603200_ref1","volume-title":"Immunobiology: The Immune System in Health and Disease","author":"Janeway","year":"2001"},{"key":"2022092013193603200_ref2","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1002\/prot.24534","article-title":"Blind prediction performance of Rosetta antibody 3.0: grafting, relaxation, 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