{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T04:22:39Z","timestamp":1770524559064,"version":"3.49.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2018,4,26]],"date-time":"2018-04-26T00:00:00Z","timestamp":1524700800000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11704140"],"award-info":[{"award-number":["11704140"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of Hubei","award":["2017CFB116"],"award-info":[{"award-number":["2017CFB116"]}]},{"DOI":"10.13039\/501100010871","name":"Thousand Talents Plan","doi-asserted-by":"crossref","award":["20205170045"],"award-info":[{"award-number":["20205170045"]}],"id":[{"id":"10.13039\/501100010871","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Non-coding RNA molecules play essential roles by interacting with other molecules to perform various biological functions. However, it is difficult to determine RNA structures due to their flexibility. At present, the number of experimentally solved RNA\u2013ligand and RNA\u2013protein structures is still insufficient. Therefore, binding sites prediction of non-coding RNA is required to understand their functions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Current RNA binding site prediction algorithms produce many false positive nucleotides that are distance away from the binding sites. Here, we present a network approach, RBind, to predict the RNA binding sites. We benchmarked RBind in RNA\u2013ligand and RNA\u2013protein datasets. The average accuracy of 0.82 in RNA\u2013ligand and 0.63 in RNA\u2013protein testing showed that this network strategy has a reliable accuracy for binding sites prediction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The codes and datasets are available at https:\/\/zhaolab.com.cn\/RBind.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty345","type":"journal-article","created":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T19:15:06Z","timestamp":1524597306000},"page":"3131-3136","source":"Crossref","is-referenced-by-count":64,"title":["RBind: computational network method to predict RNA binding sites"],"prefix":"10.1093","volume":"34","author":[{"given":"Kaili","family":"Wang","sequence":"first","affiliation":[{"name":"Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China"}]},{"given":"Yiren","family":"Jian","sequence":"additional","affiliation":[{"name":"Department of Physics, The George Washington University, Washington, DC, USA"}]},{"given":"Huiwen","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China"}]},{"given":"Chen","family":"Zeng","sequence":"additional","affiliation":[{"name":"Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China"},{"name":"Department of Physics, The George Washington University, Washington, DC, USA"}]},{"given":"Yunjie","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China"}]}],"member":"286","published-online":{"date-parts":[[2018,4,26]]},"reference":[{"key":"2023012704190710600_bty345-B1","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. Biotechnol"},{"key":"2023012704190710600_bty345-B2","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1016\/j.jmb.2004.10.055","article-title":"Network analysis of protein structures identifies functional residues","volume":"344","author":"Amitai","year":"2004","journal-title":"J. Mol. Biol"},{"key":"2023012704190710600_bty345-B3","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":"2023012704190710600_bty345-B4","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/978-1-4939-6433-8_13","article-title":"Automated RNA 3D structure prediction with RNAComposer","volume":"1490","author":"Biesiada","year":"2016","journal-title":"Methods Mol. Biol"},{"key":"2023012704190710600_bty345-B5","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gkv1479","article-title":"SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction","volume":"44","author":"Boniecki","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B7","doi-asserted-by":"crossref","first-page":"e109154","DOI":"10.1371\/journal.pone.0109154","article-title":"Break CDK2\/Cyclin E1 interface allosterically with small peptides","volume":"9","author":"Chen","year":"2014","journal-title":"PLoS One"},{"key":"2023012704190710600_bty345-B9","doi-asserted-by":"crossref","first-page":"14664","DOI":"10.1073\/pnas.0703836104","article-title":"Automated de novo prediction of native-like RNA tertiary structures","volume":"104","author":"Das","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012704190710600_bty345-B10","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/nrg3414","article-title":"Emerging methods in protein co-evolution","volume":"14","author":"de Juan","year":"2013","journal-title":"Nat. Rev. Genet"},{"key":"2023012704190710600_bty345-B11","first-page":"10444","article-title":"Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction","volume":"43","author":"De Leonardis","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B12","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/nrg3074","article-title":"Non-coding RNAs in human disease","volume":"12","author":"Esteller","year":"2011","journal-title":"Nat. Rev. Genet"},{"key":"2023012704190710600_bty345-B13","doi-asserted-by":"crossref","first-page":"a003533.","DOI":"10.1101\/cshperspect.a003533","article-title":"Riboswitches: structures and mechanisms","volume":"3","author":"Garst","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol"},{"key":"2023012704190710600_bty345-B14","doi-asserted-by":"crossref","first-page":"e92247","DOI":"10.1371\/journal.pone.0092247","article-title":"Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations","volume":"9","author":"Gong","year":"2014","journal-title":"PLoS One"},{"key":"2023012704190710600_bty345-B15","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1080\/07391102.2011.10507394","article-title":"Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation","volume":"29","author":"Gong","year":"2011","journal-title":"J. Biomol. Struct. Dyn"},{"key":"2023012704190710600_bty345-B16","doi-asserted-by":"crossref","first-page":"e45239","DOI":"10.1371\/journal.pone.0045239","article-title":"Computational study of unfolding and regulation mechanism of preQ1 riboswitches","volume":"7","author":"Gong","year":"2012","journal-title":"PLoS One"},{"key":"2023012704190710600_bty345-B17","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1016\/j.jmb.2003.08.061","article-title":"Uncovering network systems within protein structures","volume":"334","author":"Greene","year":"2003","journal-title":"J. Mol. Biol"},{"key":"2023012704190710600_bty345-B18","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1002\/jcc.23149","article-title":"A nonredundant structure dataset for benchmarking protein\u2013RNA computational docking","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput. Chem"},{"key":"2023012704190710600_bty345-B19","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1261\/rna.1270809","article-title":"Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters","volume":"15","author":"Jonikas","year":"2009","journal-title":"RNA"},{"key":"2023012704190710600_bty345-B20","doi-asserted-by":"crossref","first-page":"2891","DOI":"10.1093\/bioinformatics\/btv221","article-title":"iFoldRNA v2: folding RNA with constraints","volume":"31","author":"Krokhotin","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012704190710600_bty345-B21","doi-asserted-by":"crossref","first-page":"522","DOI":"10.4161\/rna.28826","article-title":"Computational modeling of RNA 3D structures, with the aid of experimental restraints","volume":"11","author":"Magnus","year":"2014","journal-title":"RNA Biol"},{"key":"2023012704190710600_bty345-B22","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1038\/nbt.2419","article-title":"Protein structure prediction from sequence variation","volume":"30","author":"Marks","year":"2012","journal-title":"Nat. Biotechnol"},{"key":"2023012704190710600_bty345-B23","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1261\/rna.060368.116","article-title":"RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme","volume":"23","author":"Miao","year":"2017","journal-title":"RNA"},{"key":"2023012704190710600_bty345-B24","doi-asserted-by":"crossref","first-page":"E1293","DOI":"10.1073\/pnas.1111471108","article-title":"Direct-coupling analysis of residue coevolution captures native contacts across many protein families","volume":"108","author":"Morcos","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012704190710600_bty345-B25","doi-asserted-by":"crossref","first-page":"W412","DOI":"10.1093\/nar\/gkq474","article-title":"PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences","volume":"38","author":"Murakami","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B26","doi-asserted-by":"crossref","first-page":"D130","DOI":"10.1093\/nar\/gku1063","article-title":"Rfam 12.0: updates to the RNA families database","volume":"43","author":"Nawrocki","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B27","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature06684","article-title":"The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data","volume":"452","author":"Parisien","year":"2008","journal-title":"Nature"},{"key":"2023012704190710600_bty345-B28","doi-asserted-by":"crossref","first-page":"W568","DOI":"10.1093\/nar\/gkw454","article-title":"BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins","volume":"44","author":"Paz","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B29","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1261\/rna.039834.113","article-title":"LigandRNA: computational predictor of RNA\u2013ligand interactions","volume":"19","author":"Philips","year":"2013","journal-title":"RNA"},{"key":"2023012704190710600_bty345-B31","doi-asserted-by":"crossref","first-page":"e112","DOI":"10.1093\/nar\/gks339","article-title":"Automated 3D structure composition for large RNAs","volume":"40","author":"Popenda","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B32","doi-asserted-by":"crossref","first-page":"6620","DOI":"10.1073\/pnas.0810961106","article-title":"Dynamical networks in tRNA: protein complexes","volume":"106","author":"Sethi","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012704190710600_bty345-B33","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2023012704190710600_bty345-B34","author":"Shi","year":"2016"},{"key":"2023012704190710600_bty345-B35","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1146\/annurev-biophys-070816-033920","article-title":"Theory and Modeling of RNA structure and interactions with metal ions and small molecules","volume":"46","author":"Sun","year":"2017","journal-title":"Annu. Rev. Biophys"},{"key":"2023012704190710600_bty345-B37","doi-asserted-by":"crossref","first-page":"W578","DOI":"10.1093\/nar\/gkm294","article-title":"RNABindR: a server for analyzing and predicting RNA-binding sites in proteins","volume":"35","author":"Terribilini","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B39","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gkv141","article-title":"3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B40","doi-asserted-by":"crossref","first-page":"W243","DOI":"10.1093\/nar\/gkl298","article-title":"BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences","volume":"34","author":"Wang","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B41","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1016\/j.cell.2016.03.030","article-title":"3D RNA and functional interactions from evolutionary couplings","volume":"165","author":"Weinreb","year":"2016","journal-title":"Cell"},{"key":"2023012704190710600_bty345-B42","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/ni.3456","article-title":"Tcf1 and Lef1 transcription factors establish CD8(+) T cell identity through intrinsic HDAC activity","volume":"17","author":"Xing","year":"2016","journal-title":"Nat. Immunol"},{"key":"2023012704190710600_bty345-B43","doi-asserted-by":"crossref","first-page":"e107504.","DOI":"10.1371\/journal.pone.0107504","article-title":"Vfold: a web server for RNA structure and folding thermodynamics prediction","volume":"9","author":"Xu","year":"2014","journal-title":"PLoS One"},{"key":"2023012704190710600_bty345-B44","doi-asserted-by":"crossref","first-page":"2080","DOI":"10.1002\/prot.24100","article-title":"A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction","volume":"80","author":"Yang","year":"2012","journal-title":"Proteins"},{"key":"2023012704190710600_bty345-B45","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/978-1-4939-6433-8_12","article-title":"Modeling small noncanonical RNA motifs with the Rosetta FARFAR server","volume":"1490","author":"Yesselman","year":"2016","journal-title":"Methods Mol. Biol"},{"key":"2023012704190710600_bty345-B46","doi-asserted-by":"crossref","first-page":"19016.","DOI":"10.1038\/srep19016","article-title":"Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs","volume":"6","author":"Zeng","year":"2016","journal-title":"Sci. Rep"},{"key":"2023012704190710600_bty345-B47","doi-asserted-by":"crossref","first-page":"9179","DOI":"10.1038\/srep09179","article-title":"Rsite: a computational method to identify the functional sites of noncoding RNAs","volume":"5","author":"Zeng","year":"2015","journal-title":"Sci. Rep"},{"key":"2023012704190710600_bty345-B48","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1080\/07391102.2011.10508609","article-title":"Improvements of the hierarchical approach for predicting RNA tertiary structure","volume":"28","author":"Zhao","year":"2011","journal-title":"J. Biomol. Struct. Dyn"},{"key":"2023012704190710600_bty345-B49","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1038\/srep00734","article-title":"Automated and fast building of three-dimensional RNA structures","volume":"2","author":"Zhao","year":"2012","journal-title":"Sci. Rep"},{"key":"2023012704190710600_bty345-B50","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1038\/s41598-017-03003-5","article-title":"Network analysis reveals the recognition mechanism for dimer formation of bulb-type lectins","volume":"7","author":"Zhao","year":"2017","journal-title":"Sci. Rep"},{"key":"2023012704190710600_bty345-B51","doi-asserted-by":"crossref","first-page":"D203","DOI":"10.1093\/nar\/gkv1252","article-title":"NONCODE 2016: an informative and valuable data source of long non-coding RNAs","volume":"44","author":"Zhao","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012704190710600_bty345-B52","doi-asserted-by":"crossref","first-page":"227","DOI":"10.4161\/trns.27368","article-title":"A new role for STAT3 as a regulator of chromatin topology","volume":"4","author":"Zhao","year":"2013","journal-title":"Transcription"},{"key":"2023012704190710600_bty345-B53","doi-asserted-by":"crossref","first-page":"e0124377.","DOI":"10.1371\/journal.pone.0124377","article-title":"Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T\/V mutations within the MID1 zinc-binding Bbox1 domain","volume":"10","author":"Zhao","year":"2015","journal-title":"Plos One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3131\/48921034\/bioinformatics_34_18_3131.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3131\/48921034\/bioinformatics_34_18_3131.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T08:15:22Z","timestamp":1720253722000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/18\/3131\/4987148"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,26]]},"references-count":48,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2018,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty345","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,15]]},"published":{"date-parts":[[2018,4,26]]}}}