{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T05:28:14Z","timestamp":1774070894756,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T00:00:00Z","timestamp":1684281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12074151"],"award-info":[{"award-number":["12074151"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Changzhou Sci. and Tech. Program","award":["CE20205033"],"award-info":[{"award-number":["CE20205033"]}]},{"DOI":"10.13039\/501100012223","name":"Jiangsu University of Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012223","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The rapid emergence of SARS-CoV-2 variants with multi-sites mutations is considered as a major obstacle for the development of drugs and vaccines. Although most of the functional proteins essential for SARS-CoV-2 have been determined, the understanding of the COVID-19 target-ligand interactions remains a key challenge. The old version of this COVID-19 docking server was built in 2020, and free and open to all users. Here, we present nCoVDock2, a new docking server to predict the binding modes for targets from SARS-CoV-2. First, the new server supports more targets. We replaced the modeled structures with newly resolved structures and added more potential targets of COVID-19, especially for the variants. Second, for small molecule docking, Autodock Vina was upgraded to the latest version 1.2.0, and a new scoring function was added for peptide or antibody docking. Third, the input interface and molecular visualization were updated for a better user experience. The web server, together with an extensive help and tutorial, are freely available at: https:\/\/ncovdock2.schanglab.org.cn.<\/jats:p>","DOI":"10.1093\/nar\/gkad414","type":"journal-article","created":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T10:54:50Z","timestamp":1684320890000},"page":"W365-W371","source":"Crossref","is-referenced-by-count":12,"title":["nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands"],"prefix":"10.1093","volume":"51","author":[{"given":"Kai","family":"Liu","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou \u00a0213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xufeng","family":"Lu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou \u00a0213001, China"},{"name":"Primary Biotechnology Co. , Ltd., Changzhou \u00a0213125, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hang","family":"Shi","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou \u00a0213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6380-698X","authenticated-orcid":false,"given":"Xiaojun","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou \u00a0213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9010-1750","authenticated-orcid":false,"given":"Ren","family":"Kong","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou \u00a0213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7169-9398","authenticated-orcid":false,"given":"Shan","family":"Chang","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou \u00a0213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,5,17]]},"reference":[{"key":"2023070505024038100_B1","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"2023070505024038100_B2","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"2023070505024038100_B3","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1056\/NEJMoa2002032","article-title":"Clinical characteristics of coronavirus disease 2019 in China","volume":"382","author":"Guan","year":"2020","journal-title":"N. 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