{"id":"https://openalex.org/W2966773397","doi":"https://doi.org/10.1093/bioinformatics/btz611","title":"RAG-Web: RNA structure prediction/design using RNA-As-Graphs","display_name":"RAG-Web: RNA structure prediction/design using RNA-As-Graphs","publication_year":2019,"publication_date":"2019-08-02","ids":{"openalex":"https://openalex.org/W2966773397","doi":"https://doi.org/10.1093/bioinformatics/btz611","mag":"2966773397","pmid":"https://pubmed.ncbi.nlm.nih.gov/31373604"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz611","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz611","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7999136","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084576628","display_name":"Grace Meng","orcid":null},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Grace Meng","raw_affiliation_strings":["Department of Chemistry, New York University , New York, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, New York University , New York, NY 10003, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051720704","display_name":"Marva Tariq","orcid":null},"institutions":[{"id":"https://openalex.org/I202524275","display_name":"Smith College","ror":"https://ror.org/0497crr92","country_code":"US","type":"education","lineage":["https://openalex.org/I202524275"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marva Tariq","raw_affiliation_strings":["Department of Chemistry, Smith College , Northampton, MA 01063, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Smith College , Northampton, MA 01063, USA","institution_ids":["https://openalex.org/I202524275"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100607903","display_name":"Swati Jain","orcid":"https://orcid.org/0000-0002-8625-8218"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Swati Jain","raw_affiliation_strings":["Department of Chemistry, New York University , New York, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, New York University , New York, NY 10003, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006030661","display_name":"Shereef Elmetwaly","orcid":"https://orcid.org/0000-0002-0615-7071"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shereef Elmetwaly","raw_affiliation_strings":["Department of Chemistry, New York University , New York, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, New York University , New York, NY 10003, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046513501","display_name":"Tamar Schlick","orcid":"https://orcid.org/0000-0002-2392-2062"},"institutions":[{"id":"https://openalex.org/I258800397","display_name":"New York University Shanghai","ror":"https://ror.org/02vpsdb40","country_code":"CN","type":"education","lineage":["https://openalex.org/I258800397","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Tamar Schlick","raw_affiliation_strings":["Courant Institute of Mathematical Sciences , New York University, New York, NY 10012, USA","Department of Chemistry, New York University , New York, NY 10003, USA","NYU-ECNU Center for Computational Chemistry at New York University Shanghai , Shanghai 3663, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Courant Institute of Mathematical Sciences , New York University, New York, NY 10012, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Chemistry, New York University , New York, NY 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at New York University Shanghai , Shanghai 3663, China","institution_ids":["https://openalex.org/I258800397"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5046513501"],"corresponding_institution_ids":["https://openalex.org/I258800397","https://openalex.org/I36672615","https://openalex.org/I57206974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4555,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.60435585,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"2","first_page":"647","last_page":"648"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9704999923706055,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9704999923706055,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.00559999980032444,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.004999999888241291,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6884377002716064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6613861322402954},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6243807673454285},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5321516394615173},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5161829590797424},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.46784743666648865},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46371224522590637},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.46130138635635376},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.4456753730773926},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3585888147354126},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3539714813232422},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2934843897819519},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2585541009902954},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.23667848110198975},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1647566258907318},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13109323382377625},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09560945630073547}],"concepts":[{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6884377002716064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6613861322402954},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6243807673454285},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5321516394615173},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5161829590797424},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.46784743666648865},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46371224522590637},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.46130138635635376},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.4456753730773926},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3585888147354126},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3539714813232422},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2934843897819519},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2585541009902954},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.23667848110198975},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1647566258907318},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13109323382377625},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09560945630073547}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz611","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz611","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31373604","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31373604","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7999136","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7999136","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7999136","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7999136","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G85716298","display_name":null,"funder_award_id":"R35\u2010GM122562","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1863324516","https://openalex.org/W2029817671","https://openalex.org/W2053783019","https://openalex.org/W2086115719","https://openalex.org/W2086561953","https://openalex.org/W2096327663","https://openalex.org/W2153731228","https://openalex.org/W2584434271","https://openalex.org/W2760839971","https://openalex.org/W2808795002","https://openalex.org/W2998721931"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W2581348958","https://openalex.org/W2264054990","https://openalex.org/W2986237709","https://openalex.org/W2581888268","https://openalex.org/W2902683473","https://openalex.org/W3201305480"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"launch":[2],"a":[3,119],"webserver":[4,44,140],"for":[5,101],"RNA":[6,27,40,58,90,132],"structure":[7,41,60],"prediction":[8],"and":[9,38,80,112,130,134],"design":[10,131],"corresponding":[11,63],"to":[12,25,36,61,109,122,128],"tools":[13],"developed":[14],"using":[15],"our":[16,124],"RNA-As-Graphs":[17],"(RAG)":[18],"approach.":[19],"RAG":[20,50,67,78,82,125],"uses":[21],"coarse-grained":[22],"tree":[23,53,94],"graphs":[24,75],"represent":[26],"secondary":[28,59],"structure,":[29],"allowing":[30],"the":[31],"application":[32],"of":[33,46],"graph":[34,54,95],"theory":[35],"analyze":[37],"advance":[39],"discovery.":[42],"Our":[43],"consists":[45],"three":[47],"modules:":[48],"(a)":[49],"Sampler:":[51],"samples":[52],"topologies":[55],"from":[56,73],"an":[57],"predict":[62,129],"tertiary":[64],"topologies,":[65],"(b)":[66],"Builder:":[68],"builds":[69],"three-dimensional":[70],"atomic":[71],"models":[72],"candidate":[74],"generated":[76],"by":[77,93],"Sampler,":[79],"(c)":[81],"Designer:":[83],"designs":[84],"sequences":[85],"that":[86],"fold":[87],"onto":[88],"novel":[89],"motifs":[91],"(described":[92],"topologies).":[96],"Results":[97,105],"analyses":[98],"are":[99,151],"performed":[100],"further":[102],"assessment/selection.":[103],"The":[104,139],"page":[106],"provides":[107],"links":[108],"download":[110],"results":[111],"indicates":[113],"possible":[114],"errors":[115],"encountered.":[116],"RAG-Web":[117],"offers":[118],"user-friendly":[120],"interface":[121],"utilize":[123],"software":[126],"suite":[127],"structures":[133],"sequences.":[135],"AVAILABILITY":[136],"AND":[137],"IMPLEMENTATION:":[138],"is":[141],"freely":[142],"available":[143,152],"online":[144],"at:":[145],"http://www.biomath.nyu.edu/ragtop/.":[146],"SUPPLEMENTARY":[147],"INFORMATION:":[148],"Supplementary":[149],"data":[150],"at":[153],"Bioinformatics":[154],"online.":[155]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
