{"id":"https://openalex.org/W2086561953","doi":"https://doi.org/10.1186/1748-7188-6-26","title":"ViennaRNA Package 2.0","display_name":"ViennaRNA Package 2.0","publication_year":2011,"publication_date":"2011-11-24","ids":{"openalex":"https://openalex.org/W2086561953","doi":"https://doi.org/10.1186/1748-7188-6-26","mag":"2086561953","pmid":"https://pubmed.ncbi.nlm.nih.gov/22115189"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-6-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-6-26","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-26","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-26","any_repository_has_fulltext":true},"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"]},{"id":"https://openalex.org/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Ronny Lorenz","raw_affiliation_strings":["Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, A-1090 Vienna, Austria. ronny@tbi.univie.ac.at","Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, A-1090 Vienna, Austria. ronny@tbi.univie.ac.at","institution_ids":["https://openalex.org/I129774422","https://openalex.org/I145847075"]},{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034829404","display_name":"Stephan Wolf","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":false,"raw_author_name":"Stephan H Bernhart","raw_affiliation_strings":["Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005332412","display_name":"Christian H\u00f6ner zu Siederdissen","orcid":"https://orcid.org/0000-0001-9517-5839"},"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":"Christian H\u00f6ner zu Siederdissen","raw_affiliation_strings":["Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051736898","display_name":"Hakim Tafer","orcid":null},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hakim Tafer","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, D-04107, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, D-04107, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005564950","display_name":"Christoph Flamm","orcid":"https://orcid.org/0000-0001-5500-2415"},"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":"Christoph Flamm","raw_affiliation_strings":["Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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"]},{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]},{"id":"https://openalex.org/I4210091327","display_name":"Max Planck Institute for Mathematics in the Sciences","ror":"https://ror.org/00ez2he07","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210091327"]},{"id":"https://openalex.org/I4210145647","display_name":"Fraunhofer Institute for Cell Therapy and Immunology","ror":"https://ror.org/04x45f476","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210145647","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["AT","DE","DK","US"],"is_corresponding":false,"raw_author_name":"Peter F Stadler","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, D-04107, Germany","Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, DK-1870, Denmark","Fraunhofer Institute for Cell Therapy and Immunology, Perlickstra\u00dfe 1, Gr\u00f8nneg\u00e5rdsvej 3, Leipzig, D-04103, Germany","Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, Leipzig, D-04103, Germany","Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, D-04107, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, DK-1870, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Fraunhofer Institute for Cell Therapy and Immunology, Perlickstra\u00dfe 1, Gr\u00f8nneg\u00e5rdsvej 3, Leipzig, D-04103, Germany","institution_ids":["https://openalex.org/I4210145647"]},{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, Leipzig, D-04103, Germany","institution_ids":["https://openalex.org/I4210091327"]},{"raw_affiliation_string":"Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA","institution_ids":["https://openalex.org/I1308548392"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011771355","display_name":"Ivo L. Hofacker","orcid":"https://orcid.org/0000-0001-7132-0800"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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","DK"],"is_corresponding":false,"raw_author_name":"Ivo L Hofacker","raw_affiliation_strings":["Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, DK-1870, Denmark","Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, DK-1870, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Institute for Theoretical Chemistry and Structural Biology, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, W\u00e4hringerstra\u00dfe 17/3, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5086178125"],"corresponding_institution_ids":["https://openalex.org/I129774422","https://openalex.org/I145847075"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":30.2057,"has_fulltext":true,"cited_by_count":5369,"citation_normalized_percentile":{"value":0.99844326,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"6","issue":"1","first_page":"26","last_page":"26"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9765999913215637,"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":0.9765999913215637,"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":0.011699999682605267,"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"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.0052999998442828655,"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/computer-science","display_name":"Computer science","score":0.7292363047599792},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5773099064826965},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5661941766738892},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5471732020378113},{"id":"https://openalex.org/keywords/centroid","display_name":"Centroid","score":0.5206212997436523},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.501967191696167},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.44874781370162964},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.41742825508117676},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.348422110080719},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33484262228012085},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3108193874359131},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1613817811012268},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13196486234664917},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12024083733558655}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7292363047599792},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5773099064826965},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5661941766738892},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5471732020378113},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.5206212997436523},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.501967191696167},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.44874781370162964},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.41742825508117676},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.348422110080719},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33484262228012085},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3108193874359131},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1613817811012268},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13196486234664917},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12024083733558655},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/1748-7188-6-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-6-26","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-26","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:22115189","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22115189","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:info:fedora/oai:univie.ac.at:o:245869","is_oa":true,"landing_page_url":"https://phaidra.univie.ac.at/o:245869","pdf_url":null,"source":{"id":"https://openalex.org/S4306401993","display_name":"Phaidra (Universit\u00e4t Wien)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I129774422","host_organization_name":"University of Vienna","host_organization_lineage":["https://openalex.org/I129774422"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN:1748-7188","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:26b8ef9c6640447e86261646662d1ea1","is_oa":false,"landing_page_url":"https://doaj.org/article/26b8ef9c6640447e86261646662d1ea1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"Algorithms for Molecular Biology, Vol 6, Iss 1, p 26 (2011)","raw_type":"article"},{"id":"pmh:oai:publica.fraunhofer.de:publica/227502","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/227502","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3319429","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3319429","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-6-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-6-26","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-26","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.9100000262260437,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G3118548002","display_name":null,"funder_award_id":"SFB F43","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G8011166725","display_name":null,"funder_award_id":"SFB F43 RNA","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G808786064","display_name":null,"funder_award_id":"STA 850/7-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2086561953.pdf","grobid_xml":"https://content.openalex.org/works/W2086561953.grobid-xml"},"referenced_works_count":108,"referenced_works":["https://openalex.org/W30210889","https://openalex.org/W96081152","https://openalex.org/W107776513","https://openalex.org/W954217422","https://openalex.org/W1521263928","https://openalex.org/W1543796220","https://openalex.org/W1574590441","https://openalex.org/W1585306636","https://openalex.org/W1595787500","https://openalex.org/W1605441808","https://openalex.org/W1861164398","https://openalex.org/W1950410402","https://openalex.org/W1965243792","https://openalex.org/W1966857768","https://openalex.org/W1974272811","https://openalex.org/W1976021976","https://openalex.org/W1977940795","https://openalex.org/W1981576666","https://openalex.org/W1981777358","https://openalex.org/W1984675364","https://openalex.org/W1984987205","https://openalex.org/W1988409793","https://openalex.org/W1988888548","https://openalex.org/W1989020100","https://openalex.org/W1994958179","https://openalex.org/W1995403172","https://openalex.org/W2000191287","https://openalex.org/W2000418005","https://openalex.org/W2004945910","https://openalex.org/W2009736453","https://openalex.org/W2009818318","https://openalex.org/W2015292449","https://openalex.org/W2015527441","https://openalex.org/W2017302704","https://openalex.org/W2017313617","https://openalex.org/W2018216725","https://openalex.org/W2020496613","https://openalex.org/W2022916085","https://openalex.org/W2025763720","https://openalex.org/W2033677231","https://openalex.org/W2042844155","https://openalex.org/W2051713039","https://openalex.org/W2054931730","https://openalex.org/W2061158331","https://openalex.org/W2064345118","https://openalex.org/W2065800250","https://openalex.org/W2068205681","https://openalex.org/W2069253276","https://openalex.org/W2076963640","https://openalex.org/W2085115334","https://openalex.org/W2094253263","https://openalex.org/W2095145214","https://openalex.org/W2096883982","https://openalex.org/W2098571862","https://openalex.org/W2098607715","https://openalex.org/W2098635912","https://openalex.org/W2101497682","https://openalex.org/W2101535367","https://openalex.org/W2102017611","https://openalex.org/W2106144124","https://openalex.org/W2109553965","https://openalex.org/W2111272410","https://openalex.org/W2112333437","https://openalex.org/W2113368761","https://openalex.org/W2115275409","https://openalex.org/W2117431427","https://openalex.org/W2120014163","https://openalex.org/W2120323371","https://openalex.org/W2120456037","https://openalex.org/W2121918723","https://openalex.org/W2122944508","https://openalex.org/W2125126793","https://openalex.org/W2125615424","https://openalex.org/W2126244322","https://openalex.org/W2127770193","https://openalex.org/W2129706781","https://openalex.org/W2134861301","https://openalex.org/W2136480416","https://openalex.org/W2137015675","https://openalex.org/W2137042854","https://openalex.org/W2137640371","https://openalex.org/W2140302584","https://openalex.org/W2140374128","https://openalex.org/W2143407915","https://openalex.org/W2144671815","https://openalex.org/W2145628933","https://openalex.org/W2147416962","https://openalex.org/W2151203827","https://openalex.org/W2151454989","https://openalex.org/W2151994495","https://openalex.org/W2153140501","https://openalex.org/W2154241726","https://openalex.org/W2155869782","https://openalex.org/W2159117141","https://openalex.org/W2161159766","https://openalex.org/W2162224067","https://openalex.org/W2165437648","https://openalex.org/W2165699964","https://openalex.org/W2166745309","https://openalex.org/W2170157200","https://openalex.org/W2170472690","https://openalex.org/W2171692151","https://openalex.org/W2321457778","https://openalex.org/W2400250419","https://openalex.org/W2803927613","https://openalex.org/W3122583070","https://openalex.org/W4212865600","https://openalex.org/W4234667141"],"related_works":["https://openalex.org/W576226539","https://openalex.org/W2808896479","https://openalex.org/W2133070749","https://openalex.org/W1978187259","https://openalex.org/W2889983362","https://openalex.org/W2136556521","https://openalex.org/W2982356100","https://openalex.org/W1988380385","https://openalex.org/W2071138881","https://openalex.org/W2097474307"],"abstract_inverted_index":{"BACKGROUND:":[0],"Secondary":[1],"structure":[2,77,89],"forms":[3],"an":[4,106,130],"important":[5],"intermediate":[6],"level":[7],"of":[8,10,18,74,90,102,109,117,133,142,183],"description":[9],"nucleic":[11],"acids":[12],"that":[13],"encapsulates":[14],"the":[15,19,88,91,95,99,119,123,180,184],"dominating":[16],"part":[17],"folding":[20],"energy,":[21],"is":[22,29],"often":[23],"well":[24,60],"conserved":[25],"in":[26,87,172],"evolution,":[27],"and":[28,105,122,139,151,168,187],"routinely":[30],"used":[31,51,72],"as":[32,59,61,148],"a":[33,70,113],"basis":[34],"to":[35,52,135],"explain":[36],"experimental":[37],"findings.":[38],"Based":[39],"on":[40],"carefully":[41],"measured":[42],"thermodynamic":[43,62],"parameters,":[44,98],"exact":[45],"dynamic":[46],"programming":[47],"algorithms":[48,186],"can":[49,203],"be":[50,204],"compute":[53],"ground":[54],"states,":[55],"base":[56,158],"pairing":[57,159],"probabilities,":[58,160],"properties.":[63],"RESULTS:":[64],"The":[65,194],"ViennaRNA":[66,195],"Package":[67,196],"has":[68],"been":[69],"widely":[71],"compilation":[73],"RNA":[75],"secondary":[76,166],"related":[78],"computer":[79],"programs":[80],"for":[81,163,170],"nearly":[82],"two":[83],"decades.":[84],"Major":[85],"changes":[86],"standard":[92],"energy":[93],"model,":[94],"Turner":[96],"2004":[97],"pervasive":[100],"use":[101],"multi-core":[103],"CPUs,":[104],"increasing":[107],"number":[108],"algorithmic":[110],"variants":[111],"prompted":[112],"major":[114],"technical":[115],"overhaul":[116],"both":[118],"underlying":[120],"RNAlib":[121],"interactive":[124],"user":[125],"programs.":[126],"New":[127],"features":[128],"include":[129],"expanded":[131],"repertoire":[132],"tools":[134],"assess":[136],"RNA-RNA":[137],"interactions":[138],"restricted":[140],"ensembles":[141],"structures,":[143,167],"additional":[144],"output":[145],"information":[146],"such":[147],"centroid":[149],"structures":[150,155],"maximum":[152],"expected":[153],"accuracy":[154],"derived":[156],"from":[157,206],"or":[161],"z-scores":[162],"locally":[164],"stable":[165],"support":[169],"input":[171],"fasta":[173],"format.":[174],"Updates":[175],"were":[176],"implemented":[177],"without":[178],"compromising":[179],"computational":[181],"efficiency":[182],"core":[185],"ensuring":[188],"compatibility":[189],"with":[190],"earlier":[191],"versions.":[192],"CONCLUSIONS:":[193],"2.0,":[197],"supporting":[198],"concurrent":[199],"computations":[200],"via":[201],"OpenMP,":[202],"downloaded":[205],"http://www.tbi.univie.ac.at/RNA.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":259},{"year":2025,"cited_by_count":620},{"year":2024,"cited_by_count":669},{"year":2023,"cited_by_count":515},{"year":2022,"cited_by_count":501},{"year":2021,"cited_by_count":589},{"year":2020,"cited_by_count":524},{"year":2019,"cited_by_count":374},{"year":2018,"cited_by_count":332},{"year":2017,"cited_by_count":307},{"year":2016,"cited_by_count":249},{"year":2015,"cited_by_count":200},{"year":2014,"cited_by_count":123},{"year":2013,"cited_by_count":77},{"year":2012,"cited_by_count":27}],"updated_date":"2026-06-14T07:44:22.658603","created_date":"2025-10-10T00:00:00"}
