{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:25Z","timestamp":1753875805253,"version":"3.41.2"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T00:00:00Z","timestamp":1680652800000},"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":["82173660","82003579"],"award-info":[{"award-number":["82173660","82003579"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LR21H300003","LQ21H300005"],"award-info":[{"award-number":["LR21H300003","LQ21H300005"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research and Development Program of Zhejiang Province","award":["2020C03010"],"award-info":[{"award-number":["2020C03010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Molecular clustering analysis has been developed to facilitate visual inspection in the process of structure-based virtual screening. However, traditional methods based on molecular fingerprints or molecular descriptors limit the accuracy of selecting active hit compounds, which may be attributed to the lack of representations of receptor structural and protein\u2013ligand interaction during the clustering. Here, a novel deep clustering framework named ClusterX is proposed to learn molecular representations of protein\u2013ligand complexes and cluster the ligands. In ClusterX, the graph was used to represent the protein\u2013ligand complex, and the joint optimisation can be used efficiently for learning the cluster-friendly features. Experiments on the KLIFs database show that the model can distinguish well between the binding modes of different kinase inhibitors. To validate the effectiveness of the model, the clustering results on the virtual screening dataset further demonstrated that ClusterX achieved better or more competitive performance against traditional methods, such as SIFt and extended connectivity fingerprints. This framework may provide a unique tool for clustering analysis and prove to assist computational medicinal chemists in visual decision-making.<\/jats:p>","DOI":"10.1093\/bib\/bbad126","type":"journal-article","created":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T04:30:28Z","timestamp":1680755428000},"source":"Crossref","is-referenced-by-count":5,"title":["ClusterX: a novel representation learning-based deep clustering framework for accurate visual inspection in virtual screening"],"prefix":"10.1093","volume":"24","author":[{"given":"Sikang","family":"Chen","sequence":"first","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Gao","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiexuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yufeng","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Software Technology, Zhejiang University , Hangzhou 310058 , China"},{"name":"Second Affiliated Hospital School of Medicine , and School of Public Health, , Hangzhou 310058 , China"},{"name":"Zhejiang University , and School of Public Health, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zheyuan","family":"Shen","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Xu","sequence":"additional","affiliation":[{"name":"Cancer Center of Zhejiang University , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinxin","family":"Che","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Wu","sequence":"additional","affiliation":[{"name":"Second Affiliated Hospital School of Medicine , and School of Public Health, , Hangzhou 310058 , China"},{"name":"Zhejiang University , and School of Public Health, , Hangzhou 310058 , China"},{"name":"Institute of Bioinformatics and Medical Engineering , School of Electrical and Information Engineering, , Changzhou 212003 , China"},{"name":"Jiangsu University of Technology , School of Electrical and Information Engineering, , Changzhou 212003 , China"},{"name":"College of Computer Science and Technology, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaowu","family":"Dong","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Institute of Bioinformatics and Medical Engineering , School of Electrical and Information Engineering, , Changzhou 212003 , China"},{"name":"Jiangsu University of Technology , School of Electrical and Information Engineering, , Changzhou 212003 , China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University , Hangzhou 310058 , China"},{"name":"Department of Pharmacy , the Second Affiliated Hospital, , Hangzhou 310058 , China"},{"name":"Zhejiang University School of Medicine , the Second Affiliated Hospital, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,5]]},"reference":[{"key":"2023052022112760600_ref1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.4155\/fmc.12.18","article-title":"Analysis of structure-based virtual screening studies and characterization of identified active 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