{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T12:21:14Z","timestamp":1784290874420,"version":"3.55.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T00:00:00Z","timestamp":1683158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32125007"],"award-info":[{"award-number":["32125007"]}],"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":["91940306"],"award-info":[{"award-number":["91940306"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Qilu Young Scholars\u00a0Program of Shandong University"},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2022M711846"],"award-info":[{"award-number":["2022M711846"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2022M721859"],"award-info":[{"award-number":["2022M721859"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Postdoctoral Foundation of Tsinghua\u2013Peking Center for Life Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Fundamental to post-transcriptional regulation, the in vivo binding of RNA binding proteins (RBPs) on their RNA targets heavily depends on RNA structures. To date, most methods for RBP\u2013RNA interaction prediction are based on RNA structures predicted from sequences, which do not consider the various intracellular environments and thus cannot predict cell type-specific RBP\u2013RNA interactions. Here, we present a web server PrismNet that uses a deep learning tool to integrate in vivo RNA secondary structures measured by icSHAPE experiments with RBP binding site information from UV cross-linking and immunoprecipitation in the same cell lines to predict cell type-specific RBP\u2013RNA interactions. Taking an RBP and an RNA region with sequential and structural information as input (\u2018Sequence &amp; Structure\u2019 mode), PrismNet outputs the binding probability of the RBP and this RNA region, together with a saliency map and a sequence\u2013structure integrative motif. The web server is freely available at http:\/\/prismnetweb.zhanglab.net.<\/jats:p>","DOI":"10.1093\/nar\/gkad353","type":"journal-article","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T12:26:10Z","timestamp":1683203170000},"page":"W468-W477","source":"Crossref","is-referenced-by-count":37,"title":["PrismNet: predicting protein\u2013RNA interaction using <i>in\u00a0vivo<\/i> RNA structural information"],"prefix":"10.1093","volume":"51","author":[{"given":"Yiran","family":"Xu","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing \u00a0100084, China"},{"name":"Tsinghua\u2013Peking Center for Life Sciences , Beijing \u00a0100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianghui","family":"Zhu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing \u00a0100084, China"},{"name":"Tsinghua\u2013Peking Center for Life Sciences , Beijing \u00a0100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenze","family":"Huang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing \u00a0100084, China"},{"name":"Tsinghua\u2013Peking Center for Life Sciences , Beijing \u00a0100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kui","family":"Xu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing \u00a0100084, China"},{"name":"Tsinghua\u2013Peking Center for Life Sciences , Beijing \u00a0100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Yang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing \u00a0100084, China"},{"name":"Tsinghua\u2013Peking Center for Life Sciences , Beijing \u00a0100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiangfeng\u00a0Cliff","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing \u00a0100084, China"},{"name":"Tsinghua\u2013Peking Center for Life Sciences , Beijing \u00a0100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1400-2157","authenticated-orcid":false,"given":"Lei","family":"Sun","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University , Qingdao \u00a0266237, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,4]]},"reference":[{"key":"2023070504570921000_B1","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/nrg2172","article-title":"Ribozymes, riboswitches and beyond: regulation of gene expression without proteins","volume":"8","author":"Serganov","year":"2007","journal-title":"Nat. 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