{"id":"https://openalex.org/W2071643371","doi":"https://doi.org/10.1109/bibe.2007.4375595","title":"A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots","display_name":"A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots","publication_year":2007,"publication_date":"2007-10-01","ids":{"openalex":"https://openalex.org/W2071643371","doi":"https://doi.org/10.1109/bibe.2007.4375595","mag":"2071643371"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2007.4375595","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375595","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},"type":"article","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/A5100693924","display_name":"Xiang Chen","orcid":"https://orcid.org/0000-0002-1072-6230"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiang Chen","raw_affiliation_strings":["Chinese Academy of Sciences, Beijing, Beijing, CN","[Chinese Acad. of Sci, Beijing]"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Beijing, Beijing, CN","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"[Chinese Acad. of Sci, Beijing]","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100695089","display_name":"Si\u2010Min He","orcid":"https://orcid.org/0000-0002-2434-7194"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Si-Min He","raw_affiliation_strings":["Chinese Academy of Sciences, Beijing, Beijing, CN","[Chinese Acad. of Sci, Beijing]"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Beijing, Beijing, CN","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"[Chinese Acad. of Sci, Beijing]","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076729236","display_name":"Dongbo Bu","orcid":"https://orcid.org/0000-0003-4119-4238"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong-Bo Bu","raw_affiliation_strings":["Chinese Academy of Sciences, Beijing, Beijing, CN","[Chinese Acad. of Sci, Beijing]"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Beijing, Beijing, CN","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"[Chinese Acad. of Sci, Beijing]","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029900952","display_name":"Runsheng Chen","orcid":"https://orcid.org/0000-0001-6049-8347"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Run-Sheng Chen","raw_affiliation_strings":["Institute of Biophysics, Chinese Academy and Sciences, Beijing, China","Insitute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"],"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, Chinese Academy and Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210112540"]},{"raw_affiliation_string":"Insitute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018478553","display_name":"Wen Gao","orcid":"https://orcid.org/0000-0002-8070-802X"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen Gao","raw_affiliation_strings":["Institute of Computing Technology, Chinese Academy and Sciences, Beijing, China","Institute of Computing Technology , Chinese Academy of Sciences, Beijing 100080,China)"],"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology, Chinese Academy and Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Institute of Computing Technology , Chinese Academy of Sciences, Beijing 100080,China)","institution_ids":["https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100693924"],"corresponding_institution_ids":["https://openalex.org/I19820366"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.11540806,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"11","issue":null,"first_page":"411","last_page":"417"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9858999848365784,"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":0.9840999841690063,"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":0.8320059180259705},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.7671037912368774},{"id":"https://openalex.org/keywords/greedy-algorithm","display_name":"Greedy algorithm","score":0.584798276424408},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.5797852277755737},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5107192993164062},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.45561110973358154},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.2869202792644501},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14181971549987793}],"concepts":[{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.8320059180259705},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7671037912368774},{"id":"https://openalex.org/C51823790","wikidata":"https://www.wikidata.org/wiki/Q504353","display_name":"Greedy algorithm","level":2,"score":0.584798276424408},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.5797852277755737},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5107192993164062},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.45561110973358154},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2869202792644501},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14181971549987793},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibe.2007.4375595","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375595","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.110.5797","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.110.5797","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.jdl.ac.cn/doc/2007/a flexible stem-based local search algorithm for predicting rna secondary structures including pseudoknots.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W602602481","https://openalex.org/W1519185585","https://openalex.org/W1574643310","https://openalex.org/W1584476217","https://openalex.org/W1975017903","https://openalex.org/W2004945910","https://openalex.org/W2009818318","https://openalex.org/W2011368877","https://openalex.org/W2014989101","https://openalex.org/W2025763720","https://openalex.org/W2040015982","https://openalex.org/W2044595289","https://openalex.org/W2045895660","https://openalex.org/W2054697783","https://openalex.org/W2076756368","https://openalex.org/W2086509077","https://openalex.org/W2102046276","https://openalex.org/W2104141342","https://openalex.org/W2109297587","https://openalex.org/W2117552736","https://openalex.org/W2123241418","https://openalex.org/W2148599336","https://openalex.org/W2161392566","https://openalex.org/W2167673850","https://openalex.org/W2340006107","https://openalex.org/W4234879553","https://openalex.org/W4234887284","https://openalex.org/W6704052874"],"related_works":["https://openalex.org/W3183948672","https://openalex.org/W1531601525","https://openalex.org/W1827895227","https://openalex.org/W4285104409","https://openalex.org/W4210317843","https://openalex.org/W2148035265","https://openalex.org/W4366090886","https://openalex.org/W2071643371","https://openalex.org/W4302010637","https://openalex.org/W3105465283"],"abstract_inverted_index":{"We":[0,59,90],"demonstrate":[1,123],"a":[2,26,42,63,77],"new":[3],"algorithm":[4,66,73,133,138],"named":[5],"FlexStem":[6,72,93,125],"to":[7,76,115,147],"predict":[8],"RNA":[9,53],"secondary":[10],"structures":[11],"with":[12,67],"pseudoknots.":[13,39],"Our":[14],"approach":[15],"is":[16,31,56,74],"based":[17],"on":[18,69,143],"the":[19,49,95,131],"free":[20],"energy":[21,28],"minimization":[22],"criterion,":[23],"and":[24,34,45,86,98,106,111],"utilizes":[25],"sophisticated":[27],"model":[29],"that":[30,92,124],"more":[32,36],"accurate":[33],"supports":[35],"types":[37],"of":[38,80],"By":[40],"using":[41],"\"maximal":[43],"stem\"":[44],"\"stem":[46],"merging\"":[47],"strategy,":[48],"search":[50,65],"space":[51],"for":[52],"structure":[54],"prediction":[55,141],"significantly":[57,127],"reduced.":[58],"have":[60],"also":[61],"developed":[62],"greedy":[64],"perturbation":[68],"stems.":[70],"The":[71],"applied":[75],"large":[78],"number":[79],"sequences":[81,145],"taken":[82],"from":[83],"Sprinzl,":[84],"Pseudobase":[85],"other":[87],"reliable":[88],"resource.":[89],"find":[91],"outperforms":[94],"well-known":[96],"optimal":[97,132],"heuristic":[99],"algorithms":[100,117],"such":[101],"as":[102],"Mfold,":[103],"PKNOTS,":[104],"HotKnots":[105],"ILM":[107],"in":[108,118],"overall":[109,119],"sensitivity":[110],"has":[112,139],"comparable":[113],"results":[114,142],"those":[116],"specificity.":[120],"Performance":[121],"evaluation":[122],"requires":[126],"less":[128],"time":[129],"than":[130],"PKNOTS.":[134],"In":[135],"addition,":[136],"our":[137],"better":[140],"pseudoknot-free":[144],"compared":[146],"competing":[148],"algorithms.":[149]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
