{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:22:30Z","timestamp":1764688950429},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1152,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and stability has become of great importance for characterizing their functional activity. Here, we introduce a new web application, WebRASP, that uses knowledge-based potentials for scoring RNA structures based on distance-dependent pairwise atomic interactions. This web server allows the users to upload a structure in PDB format, select several options to visualize the structure and calculate the energy profile. The server contains online help, tutorials and links to other related resources. We believe this server will be a useful tool for predicting and assessing the quality of RNA 3D structures.<\/jats:p>\n               <jats:p>Availability and implementation: The web server is available at http:\/\/melolab.org\/webrasp. It has been tested on the most popular web browsers and requires Java plugin for Jmol visualization.<\/jats:p>\n               <jats:p>Contact: \u00a0fmelo@bio.puc.cl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt441","type":"journal-article","created":{"date-parts":[[2013,8,9]],"date-time":"2013-08-09T00:48:40Z","timestamp":1376009320000},"page":"2649-2650","source":"Crossref","is-referenced-by-count":8,"title":["WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures"],"prefix":"10.1093","volume":"29","author":[{"given":"Tomas","family":"Norambuena","sequence":"first","affiliation":[{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"},{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"}]},{"given":"Jorge F.","family":"Cares","sequence":"additional","affiliation":[{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"},{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"}]},{"given":"Emidio","family":"Capriotti","sequence":"additional","affiliation":[{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"}]},{"given":"Francisco","family":"Melo","sequence":"additional","affiliation":[{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"},{"name":"1 Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, 2Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and 3Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19th st. south, Birmingham, AL 35249, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,8,7]]},"reference":[{"key":"2023012810470406000_btt441-B1","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.ceb.2012.03.006","article-title":"Small non-coding RNAs mount a silent revolution in gene expression","volume":"24","author":"Aalto","year":"2012","journal-title":"Curr. Opin. Cell Biol."},{"key":"2023012810470406000_btt441-B2","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1261\/rna.2543711","article-title":"Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation","volume":"17","author":"Bernauer","year":"2011","journal-title":"RNA"},{"key":"2023012810470406000_btt441-B3","doi-asserted-by":"crossref","first-page":"32","DOI":"10.2174\/157489308783329823","article-title":"Computational RNA structure prediction","volume":"3","author":"Capriotti","year":"2008","journal-title":"Curr. Bioinform."},{"key":"2023012810470406000_btt441-B4","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/bioinformatics\/btr093","article-title":"All-atom knowledge-based potential for RNA structure prediction and assessment","volume":"27","author":"Capriotti","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810470406000_btt441-B5","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":"2023012810470406000_btt441-B6","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.1261\/rna.2112110","article-title":"Turning limited experimental information into 3D models of RNA","volume":"16","author":"Flores","year":"2010","journal-title":"RNA"},{"key":"2023012810470406000_btt441-B7","doi-asserted-by":"crossref","first-page":"e1000406","DOI":"10.1371\/journal.pcbi.1000406","article-title":"A probabilistic model of RNA conformational space","volume":"5","author":"Frellsen","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012810470406000_btt441-B8","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1038\/nsmb.2428","article-title":"Cis-acting noncoding RNAs: friends and foes","volume":"19","author":"Guil","year":"2012","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023012810470406000_btt441-B9","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":"2023012810470406000_btt441-B10","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1126\/science.1231776","article-title":"Epigenetic regulation by long noncoding RNAs","volume":"338","author":"Lee","year":"2012","journal-title":"Science"},{"key":"2023012810470406000_btt441-B11","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":"2023012810470406000_btt441-B12","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":"2023012810470406000_btt441-B13","doi-asserted-by":"crossref","first-page":"2441","DOI":"10.1093\/bioinformatics\/btr400","article-title":"ModeRNA server: an online tool for modeling RNA 3D structures","volume":"27","author":"Rother","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810470406000_btt441-B14","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1093\/bioinformatics\/btn328","article-title":"iFoldRNA: three-dimensional RNA structure prediction and folding","volume":"24","author":"Sharma","year":"2008","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/20\/2649\/48893528\/bioinformatics_29_20_2649.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/20\/2649\/48893528\/bioinformatics_29_20_2649.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:40:31Z","timestamp":1674909631000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/20\/2649\/277453"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8,7]]},"references-count":14,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2013,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt441","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,10,15]]},"published":{"date-parts":[[2013,8,7]]}}}