{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T19:34:39Z","timestamp":1774380879445,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,12]],"date-time":"2022-02-12T00:00:00Z","timestamp":1644624000000},"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\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0712402"],"award-info":[{"award-number":["2020YFA0712402"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["61973190"],"award-info":[{"award-number":["61973190"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Shandong Provincial Key Research and Development Program [Major Scientific and Technological Innovation Project","award":["2019JZZY010423"],"award-info":[{"award-number":["2019JZZY010423"]}]},{"name":"Natural Science Foundation of Shandong Province of China","award":["ZR2020ZD25"],"award-info":[{"award-number":["ZR2020ZD25"]}]},{"name":"Innovation Method Fund of China","award":["2018IM020200"],"award-info":[{"award-number":["2018IM020200"]}]},{"name":"Tang Scholar and Program of Qilu Young Scholar of Shandong University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Protein\u2013RNA interactions play essential roles in many biological processes, including pre-mRNA processing, post-transcriptional gene regulation and RNA degradation. Accurate identification of binding sites on RNA-binding proteins (RBPs) is important for functional annotation and site-directed mutagenesis. Experimental assays to sparse RBPs are precise and convincing but also costly and time consuming. Therefore, flexible and reliable computational methods are required to recognize RNA-binding residues.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we propose PST-PRNA, a novel model for predicting RNA-binding sites (PRNA) based on protein surface topography (PST). Taking full advantage of the 3D structural information of protein, PST-PRNA creates representative topography images of the entire protein surface by mapping it onto a unit spherical surface. Four kinds of descriptors are encoded to represent residues on the surface. Then, the potential features are integrated and optimized by using deep learning models. We compile a comprehensive non-redundant RBP dataset to train and test PST-PRNA using 10-fold cross-validation. Numerous experiments demonstrate PST-PRNA learns successfully the latent structural information of protein surface. On the non-redundant dataset with sequence identity of 0.3, PST-PRNA achieves area under the receiver operating characteristic curves (AUC) value of 0.860 and Matthew\u2019s correlation coefficient value of 0.420. Furthermore, we construct a completely independent test dataset for justification and comparison. PST-PRNA achieves AUC value of 0.913 on the independent dataset, which is superior to the other state-of-the-art methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code and data are available at https:\/\/www.github.com\/zpliulab\/PST-PRNA. A web server is freely available at http:\/\/www.zpliulab.cn\/PSTPRNA.<\/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\/btac078","type":"journal-article","created":{"date-parts":[[2022,2,5]],"date-time":"2022-02-05T12:09:25Z","timestamp":1644062965000},"page":"2162-2168","source":"Crossref","is-referenced-by-count":32,"title":["PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning"],"prefix":"10.1093","volume":"38","author":[{"given":"Pengpai","family":"Li","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7742-9161","authenticated-orcid":false,"given":"Zhi-Ping","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China"}]}],"member":"286","published-online":{"date-parts":[[2022,2,12]]},"reference":[{"key":"2023020109023226300_btac078-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020109023226300_btac078-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023020109023226300_btac078-B3","doi-asserted-by":"crossref","first-page":"D425","DOI":"10.1093\/nar\/gkaa1040","article-title":"RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions","volume":"49","author":"Caudron-Herger","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023020109023226300_btac078-B4","doi-asserted-by":"crossref","first-page":"D114","DOI":"10.1093\/nar\/gkt980","article-title":"The Nucleic Acid Database: new features and capabilities","volume":"42","author":"Coimbatore Narayanan","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020109023226300_btac078-B5","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1126\/science.6879170","article-title":"Solvent-accessible surfaces of proteins and nucleic acids","volume":"221","author":"Connolly","year":"1983","journal-title":"Science"},{"key":"2023020109023226300_btac078-B6","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.molcel.2020.03.011","article-title":"How RNA-binding proteins interact with RNA: molecules and mechanisms","volume":"78","author":"Corley","year":"2020","journal-title":"Mol. 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