{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:26Z","timestamp":1772138006783,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T00:00:00Z","timestamp":1610928000000},"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\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFA0502301"],"award-info":[{"award-number":["2016YFA0502301"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFA0502800"],"award-info":[{"award-number":["2016YFA0502800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Discovering efficient drugs and identifying target proteins are still an unmet but urgent need for curing coronavirus disease 2019 (COVID-19). Protein structure-based docking is a widely applied approach for discovering active compounds against drug targets and for predicting potential targets of active compounds. However, this approach has its inherent deficiency caused by e.g. various different conformations with largely varied binding pockets adopted by proteins, or the lack of true target proteins in the database. This deficiency may result in false negative results. As a complementary approach to the protein structure-based platform for COVID-19, termed as D3Docking in our previous work, we developed in this study a ligand-based method, named D3Similarity, which is based on the molecular similarity evaluation between the submitted molecule(s) and those in an active compound database. The database is constituted by all the reported bioactive molecules against the coronaviruses, viz., severe acute respiratory syndrome coronavirus (SARS), Middle East respiratory syndrome coronavirus (MERS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human betacoronavirus 2c EMC\/2012 (HCoV-EMC), human CoV 229E (HCoV-229E) and feline infectious peritonitis virus (FIPV), some of which have target or mechanism information but some do not. Based on the two-dimensional (2D) and three-dimensional (3D) similarity evaluation of molecular structures, virtual screening and target prediction could be performed according to similarity ranking results. With two examples, we demonstrated the reliability and efficiency of D3Similarity by using 2D\u2009\u00d7\u20093D value as score for drug discovery and target prediction against COVID-19. The database, which will be updated regularly, is available free of charge at https:\/\/www.d3pharma.com\/D3Targets-2019-nCoV\/D3Similarity\/index.php.<\/jats:p>","DOI":"10.1093\/bib\/bbaa422","type":"journal-article","created":{"date-parts":[[2020,12,21]],"date-time":"2020-12-21T07:09:14Z","timestamp":1608534554000},"page":"1053-1064","source":"Crossref","is-referenced-by-count":42,"title":["Ligand-based approach for predicting drug targets and for virtual screening against COVID-19"],"prefix":"10.1093","volume":"22","author":[{"given":"Yanqing","family":"Yang","sequence":"first","affiliation":[{"name":"Shanghai Institute of Materia Medica"},{"name":"CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"}]},{"given":"Zhengdan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica in 2020. His research interest is halogen bond interaction. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"}]},{"given":"Xiaoyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanghai University of Electric Power. Her research interest is database construction. Her affiliation is with College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China"}]},{"given":"Xinben","family":"Zhang","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology. His research interest is software development. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China"}]},{"given":"Kaijie","family":"Mu","sequence":"additional","affiliation":[{"name":"Nano Science and Technology Institute, University of Science and Technology of China. Her research interest is QM\/MM calculations and molecular modeling. Her affiliation is with Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, Jiangsu, 215123, China"}]},{"given":"Yulong","family":"Shi","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica. His research interest is molecular docking method development. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"}]},{"given":"Cheng","family":"Peng","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica. His research interest is molecular dynamics. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3063-8473","authenticated-orcid":false,"given":"Zhijian","family":"Xu","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica in 2012"}]},{"given":"Weiliang","family":"Zhu","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica in 1998"}]}],"member":"286","published-online":{"date-parts":[[2021,1,18]]},"reference":[{"key":"2021032314374846000_ref1","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 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