{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T02:25:57Z","timestamp":1774491957765,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,1,8]],"date-time":"2021-01-08T00:00:00Z","timestamp":1610064000000},"content-version":"vor","delay-in-days":7,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871290"],"award-info":[{"award-number":["11871290"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61873185"],"award-info":[{"award-number":["61873185"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004806","name":"Fok Ying-Tong Education Foundation","doi-asserted-by":"crossref","award":["161003"],"award-info":[{"award-number":["161003"]}],"id":[{"id":"10.13039\/501100004806","id-type":"DOI","asserted-by":"crossref"}]},{"name":"KLMDASR"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA molecules become attractive small molecule drug targets to treat disease in recent years. Computer-aided drug design can be facilitated by detecting the RNA sites that bind small molecules. However, very limited progress has been reported for the prediction of small molecule\u2013RNA binding sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a novel method RNAsite to predict small molecule\u2013RNA binding sites using sequence profile- and structure-based descriptors. RNAsite was shown to be competitive with the state-of-the-art methods on the experimental structures of two independent test sets. When predicted structure models were used, RNAsite outperforms other methods by a large margin. The possibility of improving RNAsite by geometry-based binding pocket detection was investigated. The influence of RNA structure\u2019s flexibility and the conformational changes caused by ligand binding on RNAsite were also discussed. RNAsite is anticipated to be a useful tool for the design of RNA-targeting small molecule drugs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/yanglab.nankai.edu.cn\/RNAsite.<\/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\/btaa1092","type":"journal-article","created":{"date-parts":[[2020,12,23]],"date-time":"2020-12-23T15:24:03Z","timestamp":1608737043000},"page":"36-42","source":"Crossref","is-referenced-by-count":67,"title":["Recognition of small molecule\u2013RNA binding sites using RNA sequence and structure"],"prefix":"10.1093","volume":"37","author":[{"given":"Hong","family":"Su","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences, Nankai University , Tianjin 300071, China"}]},{"given":"Zhenling","family":"Peng","sequence":"additional","affiliation":[{"name":"Center for Applied Mathematics, Tianjin University , Tianjin 300072, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2912-7737","authenticated-orcid":false,"given":"Jianyi","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences, Nankai University , Tianjin 300071, China"}]}],"member":"286","published-online":{"date-parts":[[2021,1,8]]},"reference":[{"key":"2023051510473688300_btaa1092-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2023051510473688300_btaa1092-B2","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning","volume":"33","author":"Alipanahi","year":"2015","journal-title":"Nat. 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