{"id":"https://openalex.org/W1999775600","doi":"https://doi.org/10.1093/bioinformatics/11.6.685","title":"RNA secondary structure prediction using highly parallel computers","display_name":"RNA secondary structure prediction using highly parallel computers","publication_year":1995,"publication_date":"1995-01-01","ids":{"openalex":"https://openalex.org/W1999775600","doi":"https://doi.org/10.1093/bioinformatics/11.6.685","mag":"1999775600","pmid":"https://pubmed.ncbi.nlm.nih.gov/8808586"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/11.6.685","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/11.6.685","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","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/A5031218359","display_name":"Akihiro Nakaya","orcid":"https://orcid.org/0000-0001-8308-6177"},"institutions":[{"id":"https://openalex.org/I14396692","display_name":"Tokyo University of Information Sciences","ror":"https://ror.org/044bdx604","country_code":"JP","type":"education","lineage":["https://openalex.org/I14396692"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akihiro Nakaya","raw_affiliation_strings":["Department of Information Science, University of Tokyo, Japan","Dept. of Information Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I14396692","https://openalex.org/I161296585"]},{"raw_affiliation_string":"Dept. of Information Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005766294","display_name":"Kenji Yamamoto","orcid":"https://orcid.org/0000-0002-6831-5346"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenji Yamamoto","raw_affiliation_strings":["Department of Bacteriology, Faculty of Medicine, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan","Department of Bacteriology, Faculty of Medicine, The University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bacteriology, Faculty of Medicine, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Bacteriology, Faculty of Medicine, The University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109877761","display_name":"Akinori Yonezawa","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akinori Yonezawa","raw_affiliation_strings":["Department of Information Science, Faculty of Science, The University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Science, Faculty of Science, The University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.4325,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.81602917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"11","issue":"6","first_page":"685","last_page":"692"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9919999837875366,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9886999726295471,"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":0.6930951476097107},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.6244702339172363},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5978965759277344},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5312620997428894},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.516147255897522},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4685690701007843},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4654214084148407},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46334749460220337},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.46239173412323},{"id":"https://openalex.org/keywords/viroid","display_name":"Viroid","score":0.45918530225753784},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3848564028739929},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3561933636665344},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3238447904586792},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21084022521972656},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.15444186329841614},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1039172112941742},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08926284313201904}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6930951476097107},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.6244702339172363},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5978965759277344},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5312620997428894},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.516147255897522},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4685690701007843},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4654214084148407},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46334749460220337},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.46239173412323},{"id":"https://openalex.org/C2780781446","wikidata":"https://www.wikidata.org/wiki/Q209917","display_name":"Viroid","level":4,"score":0.45918530225753784},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3848564028739929},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3561933636665344},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3238447904586792},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21084022521972656},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.15444186329841614},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1039172112941742},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08926284313201904},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/11.6.685","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/11.6.685","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:8808586","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/8808586","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":"Computer applications in the biosciences : CABIOS","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1975806245","https://openalex.org/W2558432341","https://openalex.org/W3047450301","https://openalex.org/W2345156963","https://openalex.org/W1971402940","https://openalex.org/W2919479895","https://openalex.org/W2131054067","https://openalex.org/W3196523453","https://openalex.org/W2021868453","https://openalex.org/W2791545870"],"abstract_inverted_index":{"An":[0],"RNA":[1,23],"secondary":[2,109],"structure":[3],"prediction":[4,72],"method":[5,33],"using":[6,114],"a":[7,21,30,40,99],"highly":[8,61],"parallel":[9,31,57,100],"computer":[10],"is":[11,27,86],"reported.":[12],"We":[13],"focus":[14],"on":[15,29,128],"finding":[16],"thermodynamically":[17],"stable":[18,62,78],"structures":[19,63,110],"of":[20,39,45,49,69,108,117],"single-stranded":[22],"molecule.":[24],"Our":[25,56,124],"approach":[26],"based":[28],"combinatorial":[32],"which":[34],"calculates":[35],"the":[36,43,46,51,70,76,95,115],"free":[37,47],"energy":[38],"molecule":[41],"as":[42,121],"sum":[44],"energies":[48],"all":[50,64],"physically":[52],"possible":[53],"hydrogen":[54],"bonds.":[55],"algorithm":[58,85],"finds":[59],"many":[60],"at":[65],"once,":[66],"while":[67],"most":[68,77],"conventional":[71],"methods":[73],"find":[74],"only":[75],"structure.":[79],"The":[80],"important":[81],"idea":[82],"in":[83,98],"our":[84],"search":[87],"tree":[88],"pruning,":[89],"with":[90],"dynamic":[91],"load":[92],"balancing":[93],"across":[94],"processor":[96],"elements":[97],"computer.":[101],"Software":[102],"tools":[103],"for":[104],"visualization":[105],"and":[106],"classification":[107],"are":[111],"also":[112],"presented":[113],"sequence":[116],"cadang-cadang":[118],"coconut":[119],"viroid":[120],"an":[122],"example.":[123],"software":[125],"system":[126],"runs":[127],"CM-5.":[129]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
