{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:39:59Z","timestamp":1761863999765,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T00:00:00Z","timestamp":1564704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institute of General Medical Sciences, National Institutes of Health","award":["R35GM122562"],"award-info":[{"award-number":["R35GM122562"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We launch a webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach. RAG uses coarse-grained tree graphs to represent RNA secondary structure, allowing the application of graph theory to analyze and advance RNA structure discovery. Our webserver consists of three modules: (a) RAG Sampler: samples tree graph topologies from an RNA secondary structure to predict corresponding tertiary topologies, (b) RAG Builder: builds three-dimensional atomic models from candidate graphs generated by RAG Sampler, and (c) RAG Designer: designs sequences that fold onto novel RNA motifs (described by tree graph topologies). Results analyses are performed for further assessment\/selection. The Results page provides links to download results and indicates possible errors encountered. RAG-Web offers a user-friendly interface to utilize our RAG software suite to predict and design RNA structures and sequences.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The webserver is freely available online at: http:\/\/www.biomath.nyu.edu\/ragtop\/.<\/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\/btz611","type":"journal-article","created":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T03:14:57Z","timestamp":1564715697000},"page":"647-648","source":"Crossref","is-referenced-by-count":12,"title":["RAG-Web: RNA structure prediction\/design using RNA-As-Graphs"],"prefix":"10.1093","volume":"36","author":[{"given":"Grace","family":"Meng","sequence":"first","affiliation":[{"name":"Department of Chemistry, New York University , New York, NY 10003, USA"}]},{"given":"Marva","family":"Tariq","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Smith College , Northampton, MA 01063, USA"}]},{"given":"Swati","family":"Jain","sequence":"additional","affiliation":[{"name":"Department of Chemistry, New York University , New York, NY 10003, USA"}]},{"given":"Shereef","family":"Elmetwaly","sequence":"additional","affiliation":[{"name":"Department of Chemistry, New York University , New York, NY 10003, USA"}]},{"given":"Tamar","family":"Schlick","sequence":"additional","affiliation":[{"name":"Department of Chemistry, New York University , New York, NY 10003, USA"},{"name":"Courant Institute of Mathematical Sciences , New York University, New York, NY 10012, USA"},{"name":"NYU-ECNU Center for Computational Chemistry at New York University Shanghai , Shanghai 3663, China"}]}],"member":"286","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"key":"2023013112075285000_btz611-B1","doi-asserted-by":"crossref","first-page":"5414","DOI":"10.1093\/nar\/gkx045","article-title":"Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction","volume":"45","author":"Bayrak","year":"2017","journal-title":"Nucleic Acid Res"},{"key":"2023013112075285000_btz611-B2","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1137\/060651100","article-title":"Thermodynamic analysis of interacting nucleic acid strands","volume":"49","author":"Dirks","year":"2007","journal-title":"SIAM Rev"},{"key":"2023013112075285000_btz611-B3","doi-asserted-by":"crossref","first-page":"2926","DOI":"10.1093\/nar\/gkg365","article-title":"Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design","volume":"31","author":"Gan","year":"2003","journal-title":"Nucleic Acid Res"},{"key":"2023013112075285000_btz611-B4","doi-asserted-by":"crossref","first-page":"3587","DOI":"10.1016\/j.jmb.2017.09.017","article-title":"F-RAG: generating atomic models from RNA graphs using fragment assembly","volume":"429","author":"Jain","year":"2017","journal-title":"J. Mol. Biol"},{"author":"","key":"2023013112075285000_btz611-B15"},{"key":"2023013112075285000_btz611-B5","doi-asserted-by":"crossref","first-page":"7040","DOI":"10.1093\/nar\/gky524","article-title":"A pipeline for computational design of novel RNA-like topologies","volume":"46","author":"Jain","year":"2018","journal-title":"Nucleic Acid Res"},{"key":"2023013112075285000_btz611-B6","doi-asserted-by":"crossref","first-page":"4079","DOI":"10.1073\/pnas.1318893111","article-title":"Graph-based sampling for approximating global helical topologies of RNA","volume":"111","author":"Kim","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013112075285000_btz611-B7","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1093\/nar\/gkr629","article-title":"Predicting coaxial helical stacking in RNA junctions","volume":"40","author":"Laing","year":"2012","journal-title":"Nucleic Acid Res"},{"key":"2023013112075285000_btz611-B8","doi-asserted-by":"crossref","first-page":"e71947.","DOI":"10.1371\/journal.pone.0071947","article-title":"Predicting helical topologies in RNA junctions as tree graphs","volume":"8","author":"Laing","year":"2013","journal-title":"PLoS One"},{"key":"2023013112075285000_btz611-B9","doi-asserted-by":"crossref","first-page":"26.","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorith. Mol. Biol"},{"key":"2023013112075285000_btz611-B10","doi-asserted-by":"crossref","first-page":"9474","DOI":"10.1093\/nar\/gkv823","article-title":"RAG-3D: a search tool for RNA 3D substructures","volume":"43","author":"Zahran","year":"2015","journal-title":"Nucleic Acid Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz611\/29200957\/btz611.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/2\/647\/48991272\/btz611.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/2\/647\/48991272\/btz611.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:26:33Z","timestamp":1675200393000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/2\/647\/5543100"}},"subtitle":[],"editor":[{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,8,2]]},"references-count":11,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz611","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,1,15]]},"published":{"date-parts":[[2019,8,2]]}}}