{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T09:37:51Z","timestamp":1770457071757,"version":"3.49.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,10,26]],"date-time":"2021-10-26T00:00:00Z","timestamp":1635206400000},"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\/501100008860","name":"Wuhan University of Science and Technology","doi-asserted-by":"publisher","award":["1170035"],"award-info":[{"award-number":["1170035"]}],"id":[{"id":"10.13039\/501100008860","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82104695"],"award-info":[{"award-number":["82104695"]}],"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>\n               <jats:p>Target identification of small molecules is an important and still changeling work in the area of drug discovery, especially for botanical drug development. Indistinct understanding of the relationships of ligand\u2013protein interactions is one of the main obstacles for drug repurposing and identification of off-targets. In this study, we collected 9063 crystal structures of ligand-binding proteins released from January, 1995 to April, 2021 in PDB bank, and split the complexes into 5133 interaction pairs of ligand atoms and protein fragments (covalently linked three heavy atoms) with interatomic distance \u22645\u00a0\u00c5. The interaction pairs were grouped into ligand atoms with the same SYBYL atom type surrounding each type of protein fragment, which were further clustered via Bayesian Gaussian Mixture Model (BGMM). Gaussian distributions with ligand atoms \u226520 were identified as significant interaction patterns. Reliability of the significant interaction patterns was validated by comparing the difference of number of significant interaction patterns between the docked poses with higher and lower similarity to the native crystal structures. Fifty-one candidate targets of brucine, strychnine and icajine involved in Semen Strychni (M\u01ce Qi\u00e1n Z\u01d0) and eight candidate targets of astragaloside-IV, formononetin and calycosin-7-glucoside involved in Astragalus (Hu\u00e1ng Q\u00ed) were predicted by the significant interaction patterns, in combination with docking, which were consistent with the therapeutic effects of Semen Strychni and Astragalus for cancer and chronic pain. The new strategy in this study improves the accuracy of target identification for small molecules, which will facilitate discovery of botanical drugs.<\/jats:p>","DOI":"10.1093\/bib\/bbab425","type":"journal-article","created":{"date-parts":[[2021,9,18]],"date-time":"2021-09-18T11:08:05Z","timestamp":1631963285000},"source":"Crossref","is-referenced-by-count":8,"title":["Botanical drugs: a new strategy for structure-based target prediction"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8867-7969","authenticated-orcid":false,"given":"Xuxu","family":"Wei","sequence":"first","affiliation":[{"name":"Key laboratory of Chinese internal medicine of MOE, Dongzhimen Hospital, BUCM, Beijing, China"},{"name":"School of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiang","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zeyu","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingming","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, 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