{"id":"https://openalex.org/W3082412530","doi":"https://doi.org/10.1093/bioinformatics/btaa759","title":"A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions","display_name":"A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions","publication_year":2020,"publication_date":"2020-08-24","ids":{"openalex":"https://openalex.org/W3082412530","doi":"https://doi.org/10.1093/bioinformatics/btaa759","mag":"3082412530","pmid":"https://pubmed.ncbi.nlm.nih.gov/32866223"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa759","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/956/37947620/btaa759.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/956/37947620/btaa759.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041091147","display_name":"Alan Zammit","orcid":null},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Alan Zammit","raw_affiliation_strings":["Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008614579","display_name":"Leon Helwerda","orcid":"https://orcid.org/0000-0002-4299-466X"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Leon Helwerda","raw_affiliation_strings":["Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082957882","display_name":"Ren\u00e9 C. L. Olsthoorn","orcid":"https://orcid.org/0000-0003-0315-3005"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ren\u00e9 C L Olsthoorn","raw_affiliation_strings":["Group Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 RA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Group Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022631255","display_name":"Fons J. Verbeek","orcid":"https://orcid.org/0000-0003-2445-8158"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Fons J Verbeek","raw_affiliation_strings":["Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084555198","display_name":"Alexander P. Gultyaev","orcid":null},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Alexander P Gultyaev","raw_affiliation_strings":["Department of Viroscience, Erasmus Medical Center , Rotterdam, 3000 CA, The Netherlands","Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus Medical Center , Rotterdam, 3000 CA, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I121797337"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5084555198"],"corresponding_institution_ids":["https://openalex.org/I121797337"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9015,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.77769039,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"37","issue":"7","first_page":"956","last_page":"962"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10166","display_name":"Mosquito-borne diseases and control","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10166","display_name":"Mosquito-borne diseases and control","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.9828000068664551,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12047","display_name":"Viral Infections and Vectors","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/flavivirus","display_name":"Flavivirus","score":0.8388532400131226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5784660577774048},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5750723481178284},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5592268109321594},{"id":"https://openalex.org/keywords/untranslated-region","display_name":"Untranslated region","score":0.500652551651001},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.47905075550079346},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4725354015827179},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.40775662660598755},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.32691556215286255},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.2365362048149109},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16524457931518555}],"concepts":[{"id":"https://openalex.org/C2780568436","wikidata":"https://www.wikidata.org/wiki/Q1165479","display_name":"Flavivirus","level":3,"score":0.8388532400131226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5784660577774048},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5750723481178284},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5592268109321594},{"id":"https://openalex.org/C89604277","wikidata":"https://www.wikidata.org/wiki/Q424345","display_name":"Untranslated region","level":4,"score":0.500652551651001},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.47905075550079346},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4725354015827179},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40775662660598755},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.32691556215286255},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.2365362048149109},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16524457931518555}],"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":"D005416","descriptor_name":"Flavivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005416","descriptor_name":"Flavivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005416","descriptor_name":"Flavivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","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":6,"locations":[{"id":"doi:10.1093/bioinformatics/btaa759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa759","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/956/37947620/btaa759.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32866223","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32866223","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:eur:oai:pure.eur.nl:publications/c8f8a23b-65ed-4d13-89a4-82d197d84c20","is_oa":true,"landing_page_url":"https://pure.eur.nl/en/publications/c8f8a23b-65ed-4d13-89a4-82d197d84c20","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 37(7), 956 - 962. Oxford University Press","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8128465","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8128465","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3248641","is_oa":true,"landing_page_url":"https://hdl.handle.net/1887/3248641","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"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":"Bioinformatics","raw_type":"Article / Letter to editor"},{"id":"pmh:ul:oai:scholarlypublications.universiteitleiden.nl:item_3248641","is_oa":true,"landing_page_url":"http://hdl.handle.net/1887/3248641","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"Bioinformatics, 37(7), 956 - 962. Oxford University Press (OUP)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa759","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/956/37947620/btaa759.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5699999928474426,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3082412530.pdf","grobid_xml":"https://content.openalex.org/works/W3082412530.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1238363289","https://openalex.org/W1586410362","https://openalex.org/W1808156524","https://openalex.org/W1816614902","https://openalex.org/W1970645589","https://openalex.org/W1976765586","https://openalex.org/W1977375365","https://openalex.org/W1982850127","https://openalex.org/W1988402786","https://openalex.org/W2015869768","https://openalex.org/W2028638155","https://openalex.org/W2050892823","https://openalex.org/W2052186537","https://openalex.org/W2065843293","https://openalex.org/W2078998316","https://openalex.org/W2101221024","https://openalex.org/W2103348662","https://openalex.org/W2105070391","https://openalex.org/W2105489421","https://openalex.org/W2114312630","https://openalex.org/W2115275409","https://openalex.org/W2121918723","https://openalex.org/W2124662626","https://openalex.org/W2125452943","https://openalex.org/W2141152740","https://openalex.org/W2155140332","https://openalex.org/W2157955177","https://openalex.org/W2159117141","https://openalex.org/W2159379501","https://openalex.org/W2161534813","https://openalex.org/W2169105524","https://openalex.org/W2259471848","https://openalex.org/W2516781249","https://openalex.org/W2550011929","https://openalex.org/W2598269521","https://openalex.org/W2731509543","https://openalex.org/W2735502020","https://openalex.org/W2755048196","https://openalex.org/W2766848373","https://openalex.org/W2768218273","https://openalex.org/W2782382589","https://openalex.org/W2905474975","https://openalex.org/W2909972585","https://openalex.org/W2920743503","https://openalex.org/W2944246168","https://openalex.org/W6643124447","https://openalex.org/W6678694935","https://openalex.org/W6683697117"],"related_works":["https://openalex.org/W4318218930","https://openalex.org/W2417242754","https://openalex.org/W2276634778","https://openalex.org/W4246102828","https://openalex.org/W3037403499","https://openalex.org/W2905474975","https://openalex.org/W2080977835","https://openalex.org/W3035105908","https://openalex.org/W4234413456","https://openalex.org/W2094462429"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
