{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,26]],"date-time":"2025-07-26T08:58:41Z","timestamp":1753520321522,"version":"3.37.3"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,10,7]],"date-time":"2016-10-07T00:00:00Z","timestamp":1475798400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,10,7]],"date-time":"2016-10-07T00:00:00Z","timestamp":1475798400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology , Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/01\/COE\/09\/01"],"award-info":[{"award-number":["BT\/01\/COE\/09\/01"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential information pertaining to an RBP, like overall function annotations, are provided. The web server can be accessed at the following link: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/caps.ncbs.res.in\/rstrucfam\">http:\/\/caps.ncbs.res.in\/rstrucfam<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1289-x","type":"journal-article","created":{"date-parts":[[2016,10,7]],"date-time":"2016-10-07T04:00:40Z","timestamp":1475812840000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information"],"prefix":"10.1186","volume":"17","author":[{"given":"Pritha","family":"Ghosh","sequence":"first","affiliation":[]},{"given":"Oommen K.","family":"Mathew","sequence":"additional","affiliation":[]},{"given":"Ramanathan","family":"Sowdhamini","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,10,7]]},"reference":[{"key":"1289_CR1","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1126\/science.278.5338.609","volume":"278","author":"S Henikoff","year":"1997","unstructured":"Henikoff S, Greene E a, Pietrokovski S, Bork P, Attwood TK, Hood L. Gene families: the taxonomy of protein paralogs and chimeras. Science. 1997;278:609\u201314.","journal-title":"Science"},{"key":"1289_CR2","doi-asserted-by":"publisher","first-page":"1427","DOI":"10.1093\/nar\/30.7.1427","volume":"30","author":"V Anantharaman","year":"2002","unstructured":"Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 2002;30:1427\u201364.","journal-title":"Nucleic Acids Res"},{"key":"1289_CR3","volume-title":"Systems Biology of RNA Binding Proteins [Internet]. Yeo GW, editor","author":"S Gerstberger","year":"2014","unstructured":"Gerstberger S, Hafner M, Ascano M, Tuschl T. Systems Biology of RNA Binding Proteins [Internet]. Yeo GW, editor. Springer New York: New York, NY; 2014. Available from: http:\/\/link.springer.com\/10.1007\/978-1-4939-1221-6."},{"key":"1289_CR4","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1107\/S0907444902003487","volume":"58","author":"HM Berman","year":"2002","unstructured":"Berman HM, Westbrook J, Feng Z, Iype L, Schneider B, Zardecki C. The Nucleic Acid Database. Acta Crystallogr D Biol Crystallogr [Internet]. 2002;58:889\u201398. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12037326.","journal-title":"Acta Crystallogr D Biol Crystallogr [Internet]"},{"key":"1289_CR5","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1093\/nar\/29.4.943","volume":"29","author":"S Jones","year":"2001","unstructured":"Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM. Protein-RNA interactions: a structural analysis. Nucleic Acids Res [Internet]. 2001;29:943\u201354. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=29619&tool=pmcentrez&rendertype=abstract.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR6","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1261\/rna.5890304","volume":"10","author":"LY Han","year":"2004","unstructured":"Han LY, Cai CZ, Lo SL, Chung MCM, Chen YZ. Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. Rna [Internet]. 2004;10:355\u201368. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/14970381.","journal-title":"Rna [Internet]"},{"key":"1289_CR7","doi-asserted-by":"publisher","first-page":"W243","DOI":"10.1093\/nar\/gkl298","volume":"34","author":"L Wang","year":"2006","unstructured":"Wang L, Brown SJ, Bind N. A web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res [Internet]. 2006;34:W243\u20138.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR8","doi-asserted-by":"publisher","first-page":"e1000146","DOI":"10.1371\/journal.pcbi.1000146","volume":"4","author":"S Shazman","year":"2008","unstructured":"Shazman S, Mandel-Gutfreund Y. Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput Biol [Internet]. 2008;4:e1000146. Ohler U, editor. [cited 2013 Aug 6]. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=2518515&tool=pmcentrez&rendertype=abstract.","journal-title":"PLoS Comput Biol [Internet]"},{"key":"1289_CR9","doi-asserted-by":"publisher","first-page":"e1000832","DOI":"10.1371\/journal.pcbi.1000832","volume":"6","author":"H Kazan","year":"2010","unstructured":"Kazan H, Ray D, Chan ET, Hughes TR, Morris Q. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol [Internet]. 2010;6:e1000832. [cited 2013 Oct 24]. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=2895634&tool=pmcentrez&rendertype=abstract.","journal-title":"PLoS Comput Biol [Internet]"},{"key":"1289_CR10","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1093\/nar\/27.1.254","volume":"27","author":"TJ Hubbard","year":"1999","unstructured":"Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP: a Structural Classification of Proteins database. Nucleic Acids Res [Internet]. 1999;27:254\u20136. Available from: http:\/\/nar.oxfordjournals.org\/lookup\/doi\/10.1093\/nar\/27.1.254.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR11","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.jtbi.2012.07.013","volume":"312","author":"S Jahandideh","year":"2012","unstructured":"Jahandideh S, Srinivasasainagendra V, Zhi D. Comprehensive comparative analysis and identification of RNA-binding protein domains: Multi-class classification and feature selection. J Theor Biol [Internet]. 2012;312:65\u201375. Elsevier. Available from: http:\/\/dx.doi.org\/10.1016\/j.jtbi.2012.07.013.","journal-title":"J Theor Biol [Internet]"},{"key":"1289_CR12","doi-asserted-by":"publisher","first-page":"2928","DOI":"10.1093\/bioinformatics\/btt495","volume":"29","author":"F Agostini","year":"2013","unstructured":"Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics [Internet]. 2013;29:2928\u201330. [cited 2014 Jun 6]. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23975767.","journal-title":"Bioinformatics [Internet]"},{"key":"1289_CR13","doi-asserted-by":"publisher","first-page":"R16","DOI":"10.1186\/gb-2014-15-1-r16","volume":"15","author":"T Fukunaga","year":"2014","unstructured":"Fukunaga T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H. CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biol [Internet]. 2014;15:R16. [cited 2014 May 6]. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24447569.","journal-title":"Genome Biol [Internet]"},{"key":"1289_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gku1170","volume":"42","author":"I Paz","year":"2014","unstructured":"Paz I, Kosti I, Ares M, Cline M, Mandel-Gutfreund Y. RBPmap: A web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 2014;42:1\u20137.","journal-title":"Nucleic Acids Res"},{"key":"1289_CR15","doi-asserted-by":"publisher","first-page":"D301","DOI":"10.1093\/nar\/gkq1069","volume":"39","author":"KB Cook","year":"2011","unstructured":"Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res [Internet]. 2011;39:D301\u20138. [cited 2013 May 29]. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3013675&tool=pmcentrez&rendertype=abstract.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR16","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1261\/rna.044776.114","volume":"20","author":"X Zhang","year":"2014","unstructured":"Zhang X, Wu D, Chen L, Li X, Yang J, Fan D, et al. RAID: a comprehensive resource for human RNA-associated (RNA-RNA\/RNA-protein) interaction. RNA [Internet]. 2014;20:989\u201393. [cited 2015 Jan 17]. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24803509.","journal-title":"RNA [Internet]"},{"key":"1289_CR17","doi-asserted-by":"publisher","first-page":"D578","DOI":"10.1093\/nar\/gku903","volume":"43","author":"Y Li","year":"2015","unstructured":"Li Y, Wang C, Miao Z, Bi X, Wu D, Jin N, et al. ViRBase: a resource for virus-host ncRNA-associated interactions. Nucleic Acids Res [Internet]. 2015;43:D578\u201382. [cited 2015 Jan 17]. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25274736.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR18","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gks1199","volume":"41","author":"DD Kirsanov","year":"2013","unstructured":"Kirsanov DD, Zanegina ON, Aksianov E a, Spirin S a, Karyagina AS, Alexeevski AV. NPIDB: Nucleic acid-Protein Interaction DataBase. Nucleic Acids Res [Internet]. 2013;41:D517\u201323. [cited 2014 Jul 14]. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3531207&tool=pmcentrez&rendertype=abstract.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR19","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1093\/bioinformatics\/btp243","volume":"25","author":"S Lee","year":"2009","unstructured":"Lee S, Blundell TL. BIPA: a database for protein-nucleic acid interaction in 3D structures. Bioinformatics [Internet]. 2009;25:1559\u201360. [cited 2014 Jul 14]. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19357098.","journal-title":"Bioinformatics [Internet]"},{"key":"1289_CR20","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1002\/jmr.1061","volume":"24","author":"M Kumar","year":"2011","unstructured":"Kumar M, Gromiha MM, Raghava GPS. SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. J Mol Recognit. 2011;24:303\u201313.","journal-title":"J Mol Recognit"},{"key":"1289_CR21","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.jtbi.2005.09.018","volume":"240","author":"X Yu","year":"2006","unstructured":"Yu X, Cao J, Cai Y, Shi T, Li Y. Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. J Theor Biol. 2006;240:175\u201384.","journal-title":"J Theor Biol"},{"key":"1289_CR22","first-page":"1","volume":"1102","author":"P Ghosh","year":"2015","unstructured":"Ghosh P, Grellscheid SN, Sowdhamini R. A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities. J Biomol Struct Dyn [Internet]. 2015;1102:1\u20138. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26414300.","journal-title":"J Biomol Struct Dyn [Internet]"},{"key":"1289_CR23","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1039\/C5MB00638D","volume":"12","author":"P Ghosh","year":"2016","unstructured":"Ghosh P, Sowdhamini R. Genome-wide survey of putative RNA-binding proteins encoded in the human proteome. Mol BioSyst [Internet]. 2016;12:532\u201340. Royal Society of Chemistry. Available from: http:\/\/dx.doi.org\/10.1039\/C5MB00638D.","journal-title":"Mol BioSyst [Internet]"},{"key":"1289_CR24","doi-asserted-by":"publisher","first-page":"D304","DOI":"10.1093\/nar\/gkt1240","volume":"42","author":"NK Fox","year":"2014","unstructured":"Fox NK, Brenner SE, Chandonia J-M. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res [Internet]. 2014;42:D304\u20139. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3965108&tool=pmcentrez&rendertype=abstract.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR25","doi-asserted-by":"crossref","unstructured":"Gandhimathi A, Ghosh P, Hariharaputran S, Mathew OK, Sowdhamini R. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. Nucleic Acids Res [Internet]. 2016;44:D410\u20134. Available from: http:\/\/nar.oxfordjournals.org\/lookup\/doi\/10.1093\/nar\/gkv1205.","DOI":"10.1093\/nar\/gkv1205"},{"key":"1289_CR26","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","volume":"7","author":"SR Eddy","year":"2011","unstructured":"Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol [Internet]. 2011;7:e1002195. [cited 2013 Nov 7]. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3197634&tool=pmcentrez&rendertype=abstract.","journal-title":"PLoS Comput Biol [Internet]"},{"key":"1289_CR27","first-page":"D222","volume-title":"Eddy SR, et al","author":"RD Finn","year":"2014","unstructured":"Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY. Eddy SR, et al. Pfam: The protein families database. Nucleic Acids Res. Jan; 2014. p. D222\u201330."},{"key":"1289_CR28","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/0022-2836(90)90134-8","volume":"212","author":"A Sali","year":"1990","unstructured":"Sali A, Blundelll TL. Definition of General Topological Equivalence in Protein Structures A Procedure Involving Comparison of Properties and Dynamic Programming. J Mol Biol. 1990;212:403\u201328.","journal-title":"J Mol Biol"},{"key":"1289_CR29","doi-asserted-by":"publisher","first-page":"e10","DOI":"10.1371\/journal.pcbi.0040010","volume":"4","author":"M Menke","year":"2008","unstructured":"Menke M, Berger B, Cowen L. Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol [Internet]. 2008;4:e10. [cited 2012 Nov 23]. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=2186361&tool=pmcentrez&rendertype=abstract.","journal-title":"PLoS Comput Biol [Internet]"},{"key":"1289_CR30","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1093\/bioinformatics\/14.7.617","volume":"14","author":"K Mizuguchi","year":"1998","unstructured":"Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP. JOY: protein sequence-structure representation and analysis. Bioinformatics. 1998;14:617\u201323.","journal-title":"Bioinformatics"},{"key":"1289_CR31","doi-asserted-by":"publisher","first-page":"D530","DOI":"10.1093\/nar\/gks1050","volume":"41","author":"JA Blake","year":"2013","unstructured":"Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, et al. Gene Ontology Annotations and Resources. Nucleic Acids Res [Internet]. 2013;41:D530\u20135. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3531070&tool=pmcentrez&rendertype=abstract.","journal-title":"Nucleic Acids Res [Internet]"},{"key":"1289_CR32","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1006\/jmbi.1994.1334","volume":"238","author":"IK McDonald","year":"1994","unstructured":"McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994;238:777\u201393.","journal-title":"J Mol Biol"},{"key":"1289_CR33","doi-asserted-by":"publisher","first-page":"4940","DOI":"10.1093\/nar\/25.24.4940","volume":"25","author":"N Luscombe","year":"1997","unstructured":"Luscombe N. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res. 1997;25:4940\u20135.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1289-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1289-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1289-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:12:53Z","timestamp":1706811173000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1289-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10,7]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1289"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1289-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2016,10,7]]},"assertion":[{"value":"5 May 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 October 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"411"}}