{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T08:19:05Z","timestamp":1773130745911,"version":"3.50.1"},"reference-count":80,"publisher":"American Chemical Society (ACS)","issue":"24","license":[{"start":{"date-parts":[[2024,11,28]],"date-time":"2024-11-28T00:00:00Z","timestamp":1732752000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,11,28]],"date-time":"2024-11-28T00:00:00Z","timestamp":1732752000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,11,28]],"date-time":"2024-11-28T00:00:00Z","timestamp":1732752000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22277130"],"award-info":[{"award-number":["22277130"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22307133"],"award-info":[{"award-number":["22307133"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32071248"],"award-info":[{"award-number":["32071248"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32301050"],"award-info":[{"award-number":["32301050"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2024,12,23]]},"DOI":"10.1021\/acs.jcim.4c01594","type":"journal-article","created":{"date-parts":[[2024,11,28]],"date-time":"2024-11-28T09:30:54Z","timestamp":1732786254000},"page":"9501-9516","source":"Crossref","is-referenced-by-count":6,"title":["Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations"],"prefix":"10.1021","volume":"64","author":[{"given":"Muya","family":"Xiong","sequence":"first","affiliation":[{"name":"School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China"},{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"}]},{"given":"Tianqing","family":"Nie","sequence":"additional","affiliation":[{"name":"Lingang Laboratory, Shanghai 200031, China"},{"name":"School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China"}]},{"given":"Zhewen","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Meiyi","family":"Hu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"}]},{"given":"Haixia","family":"Su","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Hangchen","family":"Hu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1581-6155","authenticated-orcid":true,"given":"Yechun","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China"},{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6460-3095","authenticated-orcid":true,"given":"Qiang","family":"Shao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]}],"member":"316","published-online":{"date-parts":[[2024,11,28]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1038\/s41573-023-00672-y"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1002\/med.21783"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2117142119"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl4784"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42102-y"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.2c00117"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1007\/s00044-022-02951-6"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26239-2"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.9b01828"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.3c00538"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.2c00404"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1021\/acsinfecdis.3c00125"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02815-22"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05514-2"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06609-0"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add7197"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1016\/j.coviro.2021.04.006"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2020.12.005"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.2c01005"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaa107"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1039\/c2cs15297e"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1039\/D0SC02823A"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.0c03420"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1007\/s11030-021-10259-7"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1039\/D0SC04978F"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.0c05522"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202110027"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1039\/D1CC03953A"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.1c04661"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1039\/D2SC06584C"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.3c02229"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2022.103374"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1007\/s00214-005-0066-0"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1021\/jp0029109"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.2c00294"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1039\/D3SC00166K"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c01112"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.2c00151"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00201"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpca.2c06201"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.0c01063"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb4489"},{"key":"ref43\/cit43","volume-title":"Amber 2023","author":"Case D. A.","year":"2023"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00255"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1021\/j100142a004"},{"key":"ref48\/cit48","unstructured":"Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A.; Bloino, J.; Janesko, B. G.; Gomperts, R.  Gaussian 09, Revision A.02; Gaussian, Inc.: Wallingford CT, 2016."},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20857"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1021\/jp070071l"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(00)00194-9"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2020.107206"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2018.03.016"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90121-8"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130812"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00169"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23751-3"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2223-y"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00575"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202309657"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19662-4"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf7945"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1021\/acsnano.0c07383"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.7b01505"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.6b03096"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.1c00058"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.0c10770"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.1c00425"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c00693"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16954-7"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.9b02157"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1042\/BCJ20230027"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1002\/qua.26768"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmc.2020.115865"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1002\/1520-6017(200011)89:11<1404::AID-JPS4>3.0.CO;2-#"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1021\/cr950025u"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00395"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2577-1"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c01594","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c01594","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,23]],"date-time":"2024-12-23T09:12:12Z","timestamp":1734945132000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c01594"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,28]]},"references-count":80,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2024,12,23]]}},"alternative-id":["10.1021\/acs.jcim.4c01594"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.4c01594","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,28]]}}}