{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T02:57:10Z","timestamp":1777431430605,"version":"3.51.4"},"reference-count":56,"publisher":"American Chemical Society (ACS)","issue":"1","license":[{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"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":["R01GM147673"],"award-info":[{"award-number":["R01GM147673"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM149705"],"award-info":[{"award-number":["R01GM149705"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1955260"],"award-info":[{"award-number":["1955260"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2026,1,12]]},"DOI":"10.1021\/acs.jcim.5c02481","type":"journal-article","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T03:31:02Z","timestamp":1766460662000},"page":"731-743","source":"Crossref","is-referenced-by-count":1,"title":["A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein\u2013Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3506-4976","authenticated-orcid":true,"given":"Yue","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy","place":["Pittsburgh, United States"]},{"name":"University of Pittsburgh","place":["Pittsburgh, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-5702-2847","authenticated-orcid":true,"given":"Haocheng","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy","place":["Pittsburgh, United States"]},{"name":"University of Pittsburgh","place":["Pittsburgh, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2214-1397","authenticated-orcid":true,"given":"Taoyu","family":"Niu","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy","place":["Pittsburgh, United States"]},{"name":"University of Pittsburgh","place":["Pittsburgh, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9607-8229","authenticated-orcid":true,"given":"Junmei","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy","place":["Pittsburgh, United States"]},{"name":"University of Pittsburgh","place":["Pittsburgh, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2025,12,22]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00432-z"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1002\/mco2.151"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2223-y"},{"key":"ref4\/cit4","unstructured":"Antiviral Drug Discovery 2025. https:\/\/polarishub.io\/competitions\/asap-discovery\/antiviral-drug-discovery-2025 (accessed 2025)."},{"key":"ref5\/cit5","unstructured":"asap-discovery\/antiviral-ligand-poses-2025. https:\/\/polarishub.io\/competitions\/asap-discovery\/antiviral-ligand-poses-2025 (accessed 2025)."},{"key":"ref6\/cit6","unstructured":"asap-discovery\/antiviral-potency-2025. https:\/\/polarishub.io\/competitions\/asap-discovery\/antiviral-potency-2025 (accessed 2025)."},{"key":"ref7\/cit7","unstructured":"asap-discovery\/antiviral-admet-2025. https:\/\/polarishub.io\/competitions\/asap-discovery\/antiviral-admet-2025 (accessed 2025)."},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-021-00560-w"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1021\/jm0306430"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1021\/jm981037l"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0477"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1101\/2025.06.14.659707"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2210.01776"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-025-00973-x"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1101\/2024.11.19.624167"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.6b00740"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1021\/ja512751q"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.9b04233"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.9b00055"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-018-0162-6"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-052118-115325"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00934"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab054"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaf205"},{"key":"ref27\/cit27","unstructured":"Team, A. D. Ligand Poses (Blind Docking) \u2013 ASAP Polaris Blind Challenge Examples. 2025, https:\/\/github.com\/asapdiscovery\/asap-polaris-blind-challenge-examples\/blob\/main\/02.%20Ligand%20Poses%20(Blind%20Docking).ipynb."},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-3-33"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1021\/jm030644s"},{"key":"ref30\/cit30","unstructured":"Schr\u00f6dinger Suite 2017-1: Maestro, Version 11.2\n                      ; Schr\u00f6dinger, LLC: New York,\nNY, 2017."},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-013-9644-8"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00864"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00302"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.8b01026"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c00044"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"ref37\/cit37","unstructured":"Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDockTools (ADT) Version 1.5.7. http:\/\/mgltools.scripps.edu\/downloads (accessed 2025)."},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01488-1"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1016\/bs.arcc.2024.10.001"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1016\/0009-2614(95)01082-K"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1021\/jp961710n"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00255"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1063\/5.0019056"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5c00038"},{"key":"ref46\/cit46","unstructured":"Case, D. A.; Aktulga, H. M.; Belfon, K.; Ben-Shalom, I. Y.; Berryman, J. T.; Brozell, S. R.; Carvahol, F. S.; Cerutti, D. S.; Cheatham, T. E., III; Cisneros, G. A.; Cruzeiro, V. W. D.; Darden, T. A.; Forouzesh, N.; Ghazimirsaeed, M.; Giamba\u015fu, G.; Giese, T.; Gilson, M. K.; Gohlke, H.; Goetz, A. W.; Harris, J.; Huang, Z.; Izadi, S.; Izmailov, S. A.; Kasavajhala, K.; Kaymak, M. C.; Kolossv\u2019a ry, I.; Kovalenko, A.; Kurtzman, T.; Lee, T. S.; Li, P.; Li, Z.; Lin, C.; Liu, J.; Luchko, T.; Luo, R.; Machado, M.; Manathunga, M.; Merz, K. M.; Miao, Y.; Mikhailovskii, O.; Monard, G.; Nguyen, H.; O\u2019Hearn, K. A.; Onufriev, A.; Pan, F.; Pantano, S.; Rahnamoun, A.; Roe, D. R.; Roitberg, A.; Sagui, C.; Schott-Verdugo, S.; Shajan, A.; Shen, J.; Simmerling, C. L.; Skrynnikov, N. R.; Smith, J.; Swails, J.; Walker, R. C.; Wang, J.; Wang, J.; Wu, X.; Wu, Y.; Xiong, Y.; Xue, Y.; York, D. M.; Zhao, C.; Zhu, Q.; Kollman, P. A.\n                      Amber 2025\n                      ; University of California: San Francisco, 2025."},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01153"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmgm.2005.12.005"},{"key":"ref49\/cit49","unstructured":"Report on protein\u2013ligand pose prediction for\nviral proteases\nin the ASAP 2025 competition. 2025, https:\/\/docs.google.com\/document\/d\/1SGw3gklEnCv-n_zV3mRvpl4sok304032\/edit?tab=t.0#heading=h.gjdgxs (accessed 2025)."},{"key":"ref50\/cit50","unstructured":"Antiviral Drug Discovery\n2025 Results. https:\/\/polarishub.io\/competitions\/asap-discovery\/antiviral-drug-discovery-2025#competiton-results (accessed 2025)."},{"key":"ref51\/cit51","unstructured":"Vithayapalert, W. Ligand Pose Prediction by a 2-Stage Structure Prediction Framework with Fine-Tuned Boltz-1 and DiffDock-L. 2025, https:\/\/apricot-zorah-51.tiiny.site\/ (accessed 2025)."},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-53751-y"},{"key":"ref53\/cit53","unstructured":"Overview for submission for Polaris Antiviral\nCompetition 2025. https:\/\/gist.github.com\/shug3502\/f0fe74f443d1d82fa73bf869148c7cdc (accessed 2025)."},{"key":"ref54\/cit54","unstructured":"Predicted\npIC50 for the two protein targets. https:\/\/drive.google.com\/file\/d\/1axeFC3gxcVGKPDwVZO2Tyi7W9Mz2ztLN\/view (accessed 2025)."},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061007"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1021\/jm300131x"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c02481","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c02481","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T12:10:32Z","timestamp":1768565432000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c02481"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,22]]},"references-count":56,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,12]]}},"alternative-id":["10.1021\/acs.jcim.5c02481"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.5c02481","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,22]]}}}