{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T09:16:45Z","timestamp":1762766205771,"version":"build-2065373602"},"reference-count":80,"publisher":"American Chemical Society (ACS)","issue":"21","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100005946","name":"Hokkaido University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005946","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["22gm1810004","25gm1810004","25wm0325063","JP17am0101093","JP20ae0101047","JP21fk0108463","JP22ama121037","JP243fa627005"],"award-info":[{"award-number":["22gm1810004","25gm1810004","25wm0325063","JP17am0101093","JP20ae0101047","JP21fk0108463","JP22ama121037","JP243fa627005"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP20H05873"],"award-info":[{"award-number":["JP20H05873"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100025019","name":"Support for Pioneering Research Initiated by the Next Generation","doi-asserted-by":"publisher","award":["JPMJSP2119"],"award-info":[{"award-number":["JPMJSP2119"]}],"id":[{"id":"10.13039\/501100025019","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2025,11,10]]},"DOI":"10.1021\/acs.jcim.5c01396","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T12:02:23Z","timestamp":1761048143000},"page":"11925-11936","source":"Crossref","is-referenced-by-count":0,"title":["Enhanced Sampling Reveals Metastable Conformations Driving K417N-Mediated Class I Antibody Escape"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-5402-1426","authenticated-orcid":true,"given":"Xu","family":"Pan","sequence":"first","affiliation":[{"name":"Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]}]},{"given":"Takashi","family":"Tadokoro","sequence":"additional","affiliation":[{"name":"Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]},{"name":"Center of Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]},{"name":"Faculty of Pharmaceutical Sciences","place":["Yamaguchi, Japan"]},{"name":"Sanyo-Onoda City University","place":["Yamaguchi, Japan"]}]},{"given":"Taishi","family":"Onodera","sequence":"additional","affiliation":[{"name":"Research Center for Vaccine Development, National Institute of Infectious Diseases","place":["Tokyo, Japan"]},{"name":"Japan Institute for Health Security","place":["Tokyo, Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3969-302X","authenticated-orcid":true,"given":"Shunsuke","family":"Kita","sequence":"additional","affiliation":[{"name":"Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]}]},{"given":"Yoshimasa","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Research Center for Vaccine Development, National Institute of Infectious Diseases","place":["Tokyo, Japan"]},{"name":"Japan Institute for Health Security","place":["Tokyo, Japan"]}]},{"given":"Katsumi","family":"Maenaka","sequence":"additional","affiliation":[{"name":"Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]},{"name":"Center of Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4387-4790","authenticated-orcid":true,"given":"Hisham M.","family":"Dokainish","sequence":"additional","affiliation":[{"name":"Center of Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences","place":["Sapporo, Japan"]},{"name":"Hokkaido University","place":["Sapporo, Japan"]},{"name":"Research Center for Vaccine Development, National Institute of Infectious Diseases","place":["Tokyo, Japan"]},{"name":"Japan Institute for Health Security","place":["Tokyo, Japan"]}]}],"member":"316","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-101619-031510"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1910993"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf1279"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(22)00311-5"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2024.116900"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2179-y"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.08.012"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04385-3"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.03.055"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines11091472"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2852-1"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.752003"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.691715"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1126\/science.abh1139"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03398-2"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2021.04.007"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04389-z"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03324-6"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03402-9"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04411-y"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(24)00731-X"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.1c00311"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.698365"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2022.104025"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2022.797132"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1038\/s44318-024-00062-z"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2004.09.014"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.232"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1021\/jp310753z"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35641-3"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1126\/science.139.3561.1259"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10368-w"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2023.2166995"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1039\/C8RA02683A"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.8b12001"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c01246"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00038"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90121-8"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1063\/1.4813023"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1177\/10943420211006452"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00697"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506346102"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1021\/jp207931v"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1063\/1.5016222"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b00931"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22010270"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.0c11600"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.75720"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2025.05.015"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1002\/1873-3468.14990"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.1c00139"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.3390\/biom12070964"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2021.08.025"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.10416"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20945"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4067"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.4c02096"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1063\/1.460004"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(83)90014-1"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1063\/1.3073889"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1063\/5.0027873"},{"key":"ref63\/cit63","unstructured":"Schr\u00f6dinger, L. The PyMOL Molecular Graphics System, Version 2.5."},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1063\/1.2978177"},{"key":"ref66\/cit66","unstructured":"GetContacts. Available via\nthe Internet at: https:\/\/getcontacts.github.io\/."},{"key":"ref67\/cit67","unstructured":"Williams, T.; Kelley, C. Gnuplot 5.4: an interactive plotting program; 2020."},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00645"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1021\/ct300418h"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-45171-9"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04386-2"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.70658"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24514-w"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-022-01138-w"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf9302"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24435-8"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1126\/science.abc7520"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1126\/science.abc5902"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1126\/science.abd2321"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.108274"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c01396","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c01396","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T09:12:24Z","timestamp":1762765944000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c01396"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,21]]},"references-count":80,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2025,11,10]]}},"alternative-id":["10.1021\/acs.jcim.5c01396"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.5c01396","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"type":"print","value":"1549-9596"},{"type":"electronic","value":"1549-960X"}],"subject":[],"published":{"date-parts":[[2025,10,21]]}}}