{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T16:30:10Z","timestamp":1775233810453,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,6,26]],"date-time":"2017-06-26T00:00:00Z","timestamp":1498435200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81502984"],"award-info":[{"award-number":["81502984"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2016A030310421"],"award-info":[{"award-number":["2016A030310421"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Molecular-similarity searches based on two-dimensional (2D) fingerprint and three-dimensional (3D) shape represent two widely used ligand-based virtual screening (VS) methods in computer-aided drug design. 2D fingerprint-based VS utilizes the binary fragment information on a known ligand, whereas 3D shape-based VS takes advantage of geometric information for predefined features from a 3D conformation. Given their different advantages, it would be desirable to hybridize 2D fingerprint and 3D shape molecular-similarity approaches in drug discovery. Here, we presented a general hybrid molecular-similarity protocol, referred to as HybridSim, obtained by combining the 2D fingerprint- and 3D shape-based similarity search methods and evaluated its performance on 595,036 actives and decoys for 40 pharmaceutically relevant targets available in the Directory of Useful Decoys Enhanced (DUD-E). Our results showed that HybridSim significantly improved the overall performance in 40 VS projects as compared with using only 2D fingerprint and 3D shape methods. Furthermore, HybridSim-VS, the first online platform using the proposed HybridSim method coupled with 17,839,945 screenable and purchasable compounds, was developed to provide large-scale and proficient VS capabilities to experts and nonexperts in the field.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>HybridSim-VS web server is freely available at http:\/\/www.rcidm.org\/HybridSim-VS\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx418","type":"journal-article","created":{"date-parts":[[2017,6,22]],"date-time":"2017-06-22T19:40:10Z","timestamp":1498160410000},"page":"3480-3481","source":"Crossref","is-referenced-by-count":28,"title":["HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques"],"prefix":"10.1093","volume":"33","author":[{"given":"Jinling","family":"Shang","sequence":"first","affiliation":[{"name":"School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xi","family":"Dai","sequence":"additional","affiliation":[{"name":"School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yecheng","family":"Li","sequence":"additional","affiliation":[{"name":"School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Pistolozzi","sequence":"additional","affiliation":[{"name":"School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5116-7749","authenticated-orcid":false,"given":"Ling","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,6,26]]},"reference":[{"key":"2023051506352572100_btx418-B1","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1039\/C3MD00397C","article-title":"Scaffold hopping of potential anti-tumor agents by WEGA: a shape-based approach","volume":"5","author":"Ge","year":"2014","journal-title":"Med. 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