{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T01:07:47Z","timestamp":1783127267099,"version":"3.54.6"},"reference-count":171,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,11,30]],"date-time":"2021-11-30T00:00:00Z","timestamp":1638230400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61972422"],"award-info":[{"award-number":["61972422"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Vaccines have made gratifying progress in preventing the 2019 coronavirus disease (COVID-19) pandemic. However, the emergence of variants, especially the latest delta variant, has brought considerable challenges to human health. Hence, the development of robust therapeutic approaches, such as anti-COVID-19 drug design, could aid in managing the pandemic more efficiently. Some drug design strategies have been successfully applied during the COVID-19 pandemic to create and validate related lead drugs. The computational drug design methods used for COVID-19 can be roughly divided into (i) structure-based approaches and (ii) artificial intelligence (AI)-based approaches. Structure-based approaches investigate different molecular fragments and functional groups through lead drugs and apply relevant tools to produce antiviral drugs. AI-based approaches usually use end-to-end learning to explore a larger biochemical space to design antiviral drugs. This review provides an overview of the two design strategies of anti-COVID-19 drugs, the advantages and disadvantages of these strategies and discussions of future developments.<\/jats:p>","DOI":"10.1093\/bib\/bbab484","type":"journal-article","created":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T19:11:44Z","timestamp":1635189104000},"source":"Crossref","is-referenced-by-count":11,"title":["Computational anti-COVID-19 drug design: progress and challenges"],"prefix":"10.1093","volume":"23","author":[{"given":"Jinxian","family":"Wang","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University,410075, Changsha, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Heilongjiang Province Land Reclamation Headquarters General Hospital, 150001, Harbin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjuan","family":"Nie","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University,410075, Changsha, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Science, The University of Auckland,Auckland 1010, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Deng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University,410075, Changsha, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,30]]},"reference":[{"issue":"5","key":"2022012000304035800_ref1","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1001\/jama.2020.12458","article-title":"Airborne transmission of sars-cov-2: 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Chem"},{"issue":"8","key":"2022012000304035800_ref152","doi-asserted-by":"crossref","first-page":"1538","DOI":"10.1016\/j.drudis.2018.05.010","article-title":"Machine learning in chemoinformatics and drug discovery","volume":"23","author":"Lo","year":"2018","journal-title":"Drug Discov Today"},{"issue":"1","key":"2022012000304035800_ref153","first-page":"1","article-title":"e toxpred: a machine learning-based approach to estimate the toxicity of drug candidates","volume":"20","author":"Limeng","year":"2019","journal-title":"BMC Pharmacol Toxicol"},{"key":"2022012000304035800_ref154","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/978-981-15-6815-2_12","volume-title":"Computer-Aided Drug Design","author":"Akhtar","year":"2020"},{"key":"2022012000304035800_ref155","doi-asserted-by":"crossref","first-page":"110059","DOI":"10.1016\/j.chaos.2020.110059","article-title":"Applications of machine learning and artificial intelligence for covid-19 (sars-cov-2) pandemic: a 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