{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T15:08:44Z","timestamp":1793804924608,"version":"4.6.1"},"reference-count":82,"publisher":"American Chemical Society (ACS)","issue":"11","license":[{"start":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T00:00:00Z","timestamp":1779235200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM127712"],"award-info":[{"award-number":["R01GM127712"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2026,6,8]]},"DOI":"10.1021\/acs.jcim.6c00077","type":"journal-article","created":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T11:08:15Z","timestamp":1779275295000},"page":"6576-6590","source":"Crossref","is-referenced-by-count":1,"title":["Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5426-7032","authenticated-orcid":true,"given":"Hong Ha","family":"Nguyen","sequence":"first","affiliation":[{"name":"Department of Chemistry","place":["Chicago, United States"]},{"name":"Illinois Institute of Technology","place":["Chicago, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Chemistry","place":["Chicago, United States"]},{"name":"Illinois Institute of Technology","place":["Chicago, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4802-2618","authenticated-orcid":true,"given":"David D. L.","family":"Minh","sequence":"additional","affiliation":[{"name":"Department of Chemistry","place":["Chicago, United States"]},{"name":"Illinois Institute of Technology","place":["Chicago, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,5,20]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.2174\/092986710793348545"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2010.03.020"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1021\/jm030266r"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio718"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1021\/jm901137j"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1002\/cmdc.201900395"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1038\/nrd877"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1021\/jm100488w"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-021-00597-z"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1038\/nature03197"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.3390\/molecules190710150"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1063\/1.2799191"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00564"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c01288"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-023-01019-9"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1126\/science.abo7201"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","unstructured":"Passaro, S.; Corso, G.; Wohlwend, J.; Reveiz, M.; Thaler, S.; Somnath, V. R.; Getz, N.; Portnoi, T.; Roy, J.; Stark, H.; Kwabi-Addo, D.; Beaini, D.; Jaakkola, T.; Barzilay, R. Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction\n                      Mol. Biol.\n                      June 18, 2025 10.1101\/2025.06.14.659707.","DOI":"10.1101\/2025.06.14.659707"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01555"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-17480-w"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1063\/1.4751284"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1063\/1.5017136"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1088\/2399-6528\/abcbac"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.26036"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b01183"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-017-0088-4"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.8b00314"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1021\/ci900407c"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21214"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-007-9159-2"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2022.879212"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2018.02.038"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2023.9925"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1038\/s41557-021-00707-0"},{"key":"ref34\/cit34","unstructured":"MolSSI\/BioExcel COVID-19 Hub https:\/\/covid.molssi.org\/\/simulations\/#foldinghome-simulations-of-nsp5 (accessed Dec 24, 2021)."},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01518"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24664"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1021\/ci00057a005"},{"key":"ref38\/cit38","doi-asserted-by":"crossref","unstructured":"Gowers, R.; Linke, M.; Barnoud, J.; Reddy, T.; Melo, M.; Seyler, S.; Doma\u0144ski, J.; Dotson, D.; Buchoux, S.; Kenney, I.; Beckstein, O.MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In\n                      Proceedings of the Python in Science Conference\n                      2016; pp 98\u2013105.","DOI":"10.25080\/Majora-629e541a-00e"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21787"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1835675100"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2005.09.012"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1039\/D0SC04942E"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23905"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0686-2"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-00455-2"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(97)78756-3"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1098\/rspl.1895.0041"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.2307\/1412159"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1093\/biomet\/30.1-2.81"},{"key":"ref52\/cit52","first-page":"2825","volume":"12","author":"Pedregosa F.","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1007\/s00332-019-09567-y"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c00870"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1063\/1.2221680"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1021\/jm050362n"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1002\/cmdc.202200425"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1021\/ja512751q"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00900"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1038\/srep31631"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2106195118"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1021\/ct400003r"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1214330110"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c00009"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1021\/ja047115d"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0610494104"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.05.013"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.4c01073"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20033"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2018.05.061"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1021\/acsmedchemlett.4c00146"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1021\/bi00027a007"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1021\/jm061277y"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003302"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-018-0143-9"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.25180"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1021\/ct700301q"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.3390\/app9214538"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.3390\/molecules30163361"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-025-01428-y"},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1716"},{"key":"ref82\/cit82","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-025-01124-5"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c00077","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c00077","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T08:11:24Z","timestamp":1780906284000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.6c00077"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,20]]},"references-count":82,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,6,8]]}},"alternative-id":["10.1021\/acs.jcim.6c00077"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c00077","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.15001142\/v1","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.15001142\/v2","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,20]]}}}