{"doi":"10.1093/bioinformatics/btaa1092","title":"Recognition of small molecule–RNA binding sites using RNA sequence and structure","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–RNA 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–RNA 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’s 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>","journal":"Bioinformatics","year":2021,"id":632816,"datarank":0.6515708132780527,"base_score":4.343805421853684,"endowment":4.343805421853684,"self_citation_contribution":0.6515708132780527,"citation_network_contribution":0.0,"self_endowment_contribution":0.6515708132780527,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":76,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":105705,"name":"Zhenling Peng","orcid":"0000-0003-0303-6693","position":1,"is_corresponding":false},{"id":105702,"name":"Jianyi Yang","orcid":"0000-0003-2912-7737","position":2,"is_corresponding":false},{"id":14096,"name":"Hong Su","orcid":"0000-0003-2842-5003","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Recognition of small molecule–RNA binding sites using RNA sequence and structure","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–RNA 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–RNA 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’s 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>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"33416863","pmcid":"PMC8034527","openalex_id":null,"authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"11871290","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"61873185","title":null},{"funder_name":"Fok Ying-Tong Education Foundation","grant_id":"161003","title":null},{"funder_name":"KLMDASR","grant_id":"","title":null}],"total_grants":4,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"hybrid","license":"cc-by-nc","oa_locations":[{"url":"https://academic.oup.com/bioinformatics/article-pdf/37/1/36/37005829/btaa1092.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa1092/35906225/btaa1092.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/37/1/36/50321544/btaa1092.pdf","host_type":"publisher"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8034527","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8034527","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8034527?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":[],"mesh_terms":[],"keywords":[],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T10:24:11.776421Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}