{"id":"https://openalex.org/W2108852439","doi":"https://doi.org/10.1109/bibe.2003.1188924","title":"A fast algorithm for RNA secondary structure prediction including pseudoknots","display_name":"A fast algorithm for RNA secondary structure prediction including pseudoknots","publication_year":2003,"publication_date":"2003-11-21","ids":{"openalex":"https://openalex.org/W2108852439","doi":"https://doi.org/10.1109/bibe.2003.1188924","mag":"2108852439"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2003.1188924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188924","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5091493314","display_name":"Fariza Tahi","orcid":"https://orcid.org/0000-0002-3975-5668"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"F. Tahi","raw_affiliation_strings":["La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France","[La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I88467170"]},{"raw_affiliation_string":"[La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France]","institution_ids":["https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002907739","display_name":"St\u00e9fan Engelen","orcid":"https://orcid.org/0000-0003-0003-1192"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S. Engelen","raw_affiliation_strings":["La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France","[La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926","https://openalex.org/I88467170"]},{"raw_affiliation_string":"[La.M.I.-UMR 8042, CNRS/Universite dEvry-Val dEssonne/Genopole, Evry, France]","institution_ids":["https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105346792","display_name":"Mireille R\u00e9gnier","orcid":"https://orcid.org/0000-0001-9566-0105"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"M. Regnier","raw_affiliation_strings":["INRIA Rocquencourt, Le Chesnay, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Rocquencourt, Le Chesnay, France","institution_ids":["https://openalex.org/I1326498283"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.3226,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.83466733,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"3","issue":null,"first_page":"11","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9977999925613403,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9857000112533569,"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/pseudoknot","display_name":"Pseudoknot","score":0.9764274954795837},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6364400386810303},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6336185932159424},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5898640155792236},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5539706945419312},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.507961094379425},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.43378305435180664},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.373664915561676},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14583662152290344},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12992051243782043}],"concepts":[{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.9764274954795837},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6364400386810303},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6336185932159424},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5898640155792236},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5539706945419312},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.507961094379425},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.43378305435180664},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.373664915561676},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14583662152290344},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12992051243782043},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2003.1188924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188924","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W128568968","https://openalex.org/W1495973157","https://openalex.org/W1519185585","https://openalex.org/W1537127938","https://openalex.org/W1554186332","https://openalex.org/W1947795940","https://openalex.org/W1993968482","https://openalex.org/W2003004847","https://openalex.org/W2006619391","https://openalex.org/W2009818318","https://openalex.org/W2012994142","https://openalex.org/W2025763720","https://openalex.org/W2027593176","https://openalex.org/W2028574527","https://openalex.org/W2033556990","https://openalex.org/W2033680099","https://openalex.org/W2043020016","https://openalex.org/W2053783511","https://openalex.org/W2061158331","https://openalex.org/W2075702353","https://openalex.org/W2078476938","https://openalex.org/W2098341656","https://openalex.org/W2102225325","https://openalex.org/W2106882534","https://openalex.org/W2117552736","https://openalex.org/W2119407097","https://openalex.org/W2123241418","https://openalex.org/W2134453550","https://openalex.org/W2136353426","https://openalex.org/W2137356209","https://openalex.org/W2140651796","https://openalex.org/W2144660787","https://openalex.org/W2151538750","https://openalex.org/W2398951942","https://openalex.org/W4234387367","https://openalex.org/W4234667141","https://openalex.org/W4251866352","https://openalex.org/W6632079549","https://openalex.org/W6674750218","https://openalex.org/W6675352923","https://openalex.org/W6678211562"],"related_works":["https://openalex.org/W2954092143","https://openalex.org/W2148725278","https://openalex.org/W2159621058","https://openalex.org/W4225160382","https://openalex.org/W1583489351","https://openalex.org/W2135373808","https://openalex.org/W2105081912","https://openalex.org/W2796011749","https://openalex.org/W1997175692","https://openalex.org/W2059090778"],"abstract_inverted_index":{"Many":[0],"important":[1],"RNA":[2,52],"molecules":[3],"contain":[4],"pseudoknots,":[5,142],"which":[6,86],"are":[7,29,39,69,100,105],"generally":[8],"excluded":[9],"by":[10],"the":[11,14,49,64,79,90,114],"definition":[12],"of":[13,51,58,92,113],"secondary":[15,26,53,138],"structure,":[16],"mainly":[17],"for":[18,25,48],"computational":[19],"reasons.":[20],"Still,":[21],"most":[22],"existing":[23],"algorithms":[24],"structure":[27],"prediction":[28,50],"not":[30,40],"satisfactory":[31],"in":[32,108,118],"results":[33],"and":[34,81,128],"complexities,":[35],"even":[36],"when":[37,96],"pseudoknots":[38,104],"allowed.":[41],"We":[42],"present":[43],"an":[44],"algorithm,":[45],"called":[46],"P-DCFold,":[47],"structures":[54],"including":[55,140],"all":[56],"kinds":[57],"pseudoknots.":[59],"It":[60],"is":[61,94],"based":[62],"on":[63],"comparative":[65],"approach.":[66,83],"The":[67,103],"helices":[68,99],"searched":[70,101,107],"recursively,":[71],"from":[72],"more":[73],"\"likely\"":[74],"to":[75,88,126],"less":[76,132],"\"likely\",":[77],"using":[78],"\"Divide":[80],"Conquer\"":[82],"This":[84],"approach,":[85],"allows":[87],"limit":[89],"amount":[91],"searching,":[93],"possible":[95],"only":[97],"non-interleaved":[98],"for.":[102],"therefore":[106],"several":[109],"steps,":[110],"each":[111],"helix":[112],"pseudoknot":[115],"being":[116],"selected":[117],"a":[119],"different":[120],"step.":[121],"P-DCFold":[122],"has":[123],"been":[124,144],"applied":[125],"tmRNA":[127],"RnaseP":[129],"sequences.":[130],"In":[131],"than":[133],"two":[134],"seconds,":[135],"their":[136,141],"respective":[137],"structures,":[139],"have":[143],"recovered":[145],"very":[146],"efficiently.":[147]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
