{"id":"https://openalex.org/W2177307286","doi":"https://doi.org/10.1093/nar/gkv1186","title":"InterRNA: a database of base interactions in RNA structures","display_name":"InterRNA: a database of base interactions in RNA structures","publication_year":2015,"publication_date":"2015-11-08","ids":{"openalex":"https://openalex.org/W2177307286","doi":"https://doi.org/10.1093/nar/gkv1186","mag":"2177307286","pmid":"https://pubmed.ncbi.nlm.nih.gov/26553798"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkv1186","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv1186","pdf_url":"https://academic.oup.com/nar/article-pdf/44/D1/D266/9482906/gkv1186.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/44/D1/D266/9482906/gkv1186.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006208366","display_name":"Sri Devan Appasamy","orcid":"https://orcid.org/0000-0001-6609-3535"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Sri Devan Appasamy","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048356979","display_name":"Hazrina Yusof Hamdani","orcid":"https://orcid.org/0000-0003-3973-9921"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Hazrina Yusof Hamdani","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014901980","display_name":"Effirul Ikhwan Ramlan","orcid":"https://orcid.org/0000-0002-8150-4782"},"institutions":[{"id":"https://openalex.org/I33849332","display_name":"University of Malaya","ror":"https://ror.org/00rzspn62","country_code":"MY","type":"education","lineage":["https://openalex.org/I33849332"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Effirul Ikhwan Ramlan","raw_affiliation_strings":["Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia","institution_ids":["https://openalex.org/I33849332"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070763648","display_name":"Mohd Firdaus\u2010Raih","orcid":"https://orcid.org/0000-0003-4275-4663"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]}],"countries":["MY"],"is_corresponding":true,"raw_author_name":"Mohd Firdaus-Raih","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia firdaus@mfrlab.org","Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia","School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia firdaus@mfrlab.org","institution_ids":["https://openalex.org/I885383172"]},{"raw_affiliation_string":"Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia","institution_ids":["https://openalex.org/I885383172"]},{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5070763648"],"corresponding_institution_ids":["https://openalex.org/I885383172"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.9034,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.74921742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"44","issue":"D1","first_page":"D266","last_page":"D271"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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":0.9994999766349792,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.7689471244812012},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6276109218597412},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6029158234596252},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49858999252319336},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26217585802078247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2575374245643616},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11483114957809448}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7689471244812012},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6276109218597412},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6029158234596252},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49858999252319336},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26217585802078247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2575374245643616},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11483114957809448}],"mesh":[{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkv1186","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv1186","pdf_url":"https://academic.oup.com/nar/article-pdf/44/D1/D266/9482906/gkv1186.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:26553798","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26553798","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:3680761","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4702846","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:44/D1/D266","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/D1/D266","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkv1186","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv1186","pdf_url":"https://academic.oup.com/nar/article-pdf/44/D1/D266/9482906/gkv1186.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1971957619","https://openalex.org/W1983534198","https://openalex.org/W1986965497","https://openalex.org/W1992105696","https://openalex.org/W1992852587","https://openalex.org/W1995554116","https://openalex.org/W2006640104","https://openalex.org/W2009555898","https://openalex.org/W2013902881","https://openalex.org/W2018838912","https://openalex.org/W2020657839","https://openalex.org/W2032568704","https://openalex.org/W2055688390","https://openalex.org/W2058276221","https://openalex.org/W2070166301","https://openalex.org/W2073149987","https://openalex.org/W2085226685","https://openalex.org/W2090007205","https://openalex.org/W2093705507","https://openalex.org/W2098431846","https://openalex.org/W2104420868","https://openalex.org/W2106246926","https://openalex.org/W2108927984","https://openalex.org/W2122377457","https://openalex.org/W2127093900","https://openalex.org/W2134425918","https://openalex.org/W2147128567","https://openalex.org/W2150404344","https://openalex.org/W2151313206","https://openalex.org/W2151973282","https://openalex.org/W2168708922","https://openalex.org/W2169751581","https://openalex.org/W2171975065","https://openalex.org/W2172206224"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802","https://openalex.org/W4234157524"],"abstract_inverted_index":{"A":[0],"major":[1],"component":[2],"of":[3,24,59,70,80,102,112,128],"RNA":[4,53,61,86,115],"structure":[5],"stabilization":[6],"are":[7,73],"the":[8,13,48,81,92,103,109,129],"hydrogen":[9,76],"bonded":[10],"interactions":[11,26,141],"between":[12],"base":[14,25],"residues.":[15],"The":[16,78],"importance":[17],"and":[18,41,95,106],"biological":[19],"relevance":[20],"for":[21,68,131,142],"large":[22],"clusters":[23,69],"can":[27],"be":[28],"much":[29],"more":[30],"easily":[31],"investigated":[32],"when":[33],"their":[34],"occurrences":[35],"have":[36],"been":[37],"systematically":[38],"detected,":[39],"catalogued":[40],"compared.":[42],"In":[43],"this":[44],"paper,":[45],"we":[46],"describe":[47],"database":[49,82,104],"InterRNA":[50,121],"(INTERactions":[51],"in":[52],"structures":[54],"database-http://mfrlab.org/interrna/)":[55],"that":[56,72,120],"contains":[57],"records":[58,67],"known":[60,132],"3D":[62,116],"motifs":[63,117,133],"as":[64,66,134,136],"well":[65,135],"bases":[71],"interconnected":[74],"by":[75,91],"bonds.":[77],"contents":[79],"were":[83],"compiled":[84],"from":[85],"structural":[87],"annotations":[88,130],"carried":[89],"out":[90],"NASSAM":[93],"(http://mfrlab.org/grafss/nassam)":[94],"COGNAC":[96],"(http://mfrlab.org/grafss/cognac)":[97],"computer":[98],"programs.":[99],"An":[100],"analysis":[101],"content":[105],"comparisons":[107],"with":[108],"existing":[110],"corpus":[111],"knowledge":[113],"regarding":[114],"clearly":[118],"show":[119],"is":[122],"able":[123,137],"to":[124,138],"provide":[125,139],"an":[126],"extension":[127],"novel":[140],"further":[143],"investigations.":[144]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}