{"id":"https://openalex.org/W2126006277","doi":"https://doi.org/10.1093/bioinformatics/bts466","title":"Folding RNA/DNA hybrid duplexes","display_name":"Folding RNA/DNA hybrid duplexes","publication_year":2012,"publication_date":"2012-07-24","ids":{"openalex":"https://openalex.org/W2126006277","doi":"https://doi.org/10.1093/bioinformatics/bts466","mag":"2126006277","pmid":"https://pubmed.ncbi.nlm.nih.gov/22829626"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts466","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts466","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086178125","display_name":"Ronny Lorenz","orcid":"https://orcid.org/0000-0002-2144-698X"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Ronny Lorenz","raw_affiliation_strings":["1 Institute for Theoretical Chemistry, University of Vienna, 2Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria and 3Department of Bioinformatics, University of Leipzig, Haertelstra\u00dfe 16-18, 04109 Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Theoretical Chemistry, University of Vienna, 2Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria and 3Department of Bioinformatics, University of Leipzig, Haertelstra\u00dfe 16-18, 04109 Leipzig, Germany","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011771355","display_name":"Ivo L. Hofacker","orcid":"https://orcid.org/0000-0001-7132-0800"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Ivo L. Hofacker","raw_affiliation_strings":["1 Institute for Theoretical Chemistry, University of Vienna, 2Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria and 3Department of Bioinformatics, University of Leipzig, Haertelstra\u00dfe 16-18, 04109 Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Theoretical Chemistry, University of Vienna, 2Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria and 3Department of Bioinformatics, University of Leipzig, Haertelstra\u00dfe 16-18, 04109 Leipzig, Germany","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"last","author":{"id":null,"display_name":"Stephan H. Bernhart","orcid":null},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Stephan H. Bernhart","raw_affiliation_strings":["1 Institute for Theoretical Chemistry, University of Vienna, 2Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria and 3Department of Bioinformatics, University of Leipzig, Haertelstra\u00dfe 16-18, 04109 Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Theoretical Chemistry, University of Vienna, 2Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria and 3Department of Bioinformatics, University of Leipzig, Haertelstra\u00dfe 16-18, 04109 Leipzig, Germany","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086178125"],"corresponding_institution_ids":["https://openalex.org/I129774422"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6137,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.66468273,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"19","first_page":"2530","last_page":"2531"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.7860000133514404,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.7860000133514404,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.14880000054836273,"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":0.007199999876320362,"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/rna","display_name":"RNA","score":0.8076989650726318},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.698244035243988},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6015272736549377},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.536626398563385},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5026652812957764},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.43555307388305664},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4195854663848877},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3181404173374176},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29194867610931396},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2611192464828491},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11608609557151794},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08697178959846497}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.8076989650726318},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.698244035243988},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6015272736549377},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.536626398563385},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5026652812957764},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.43555307388305664},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4195854663848877},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3181404173374176},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29194867610931396},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2611192464828491},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11608609557151794},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08697178959846497},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts466","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts466","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:22829626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22829626","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:CiteSeerX.psu:10.1.1.935.7917","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.935.7917","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/07/24/bioinformatics.bts466.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W30210889","https://openalex.org/W1595069818","https://openalex.org/W1967706132","https://openalex.org/W1968789240","https://openalex.org/W1975847255","https://openalex.org/W1978139942","https://openalex.org/W1983008595","https://openalex.org/W1990476811","https://openalex.org/W1996425563","https://openalex.org/W2010759469","https://openalex.org/W2086561953","https://openalex.org/W2129706781","https://openalex.org/W2161159766"],"related_works":["https://openalex.org/W2417242754","https://openalex.org/W1977413761","https://openalex.org/W2076804805","https://openalex.org/W2038598202","https://openalex.org/W2047737550","https://openalex.org/W2111497364","https://openalex.org/W2172459784","https://openalex.org/W2538843585","https://openalex.org/W2219498660","https://openalex.org/W2145832146"],"abstract_inverted_index":{"MOTIVATION:":[0],"While":[1],"there":[2],"are":[3,84],"numerous":[4],"programs":[5],"that":[6,16],"can":[7],"predict":[8],"RNA":[9],"or":[10],"DNA":[11],"secondary":[12],"structures,":[13],"a":[14],"program":[15],"predicts":[17],"RNA/DNA":[18,48,73],"hetero-dimers":[19],"is":[20],"still":[21],"missing.":[22],"The":[23],"lack":[24],"of":[25,43,45,69,72],"easy":[26],"to":[27,56],"use":[28],"tools":[29],"for":[30,39,66],"predicting":[31],"their":[32],"structure":[33,71],"may":[34],"be":[35],"in":[36],"part":[37],"responsible":[38],"the":[40,57,67,70],"small":[41],"number":[42],"reports":[44],"biologically":[46],"relevant":[47],"hetero-dimers.":[49,74],"RESULTS:":[50],"We":[51],"present":[52],"here":[53],"an":[54],"extension":[55],"widely":[58],"used":[59],"ViennaRNA":[60],"Package":[61],"(Lorenz":[62],"et":[63],"al.,":[64],"2011)":[65],"prediction":[68],"AVAILABILITY:":[75],"http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html":[76],"CONTACT:":[77],"ronny@tbi.univie.ac.at,":[78],"berni@bioinf.uni-leipzig.de":[79],"SUPPLEMENTARY":[80],"INFORMATION:":[81],"Supplementary":[82],"data":[83],"available":[85],"at":[86],"Bioinformatics":[87],"online.":[88]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3}],"updated_date":"2026-07-21T08:15:58.654021","created_date":"2025-10-10T00:00:00"}