{"id":"https://openalex.org/W2088387037","doi":"https://doi.org/10.1109/cibcb.2010.5510321","title":"Expanded study of efn2 thermodynamic model performance on RnaPredict, an evolutionary algorithm for RNA folding","display_name":"Expanded study of efn2 thermodynamic model performance on RnaPredict, an evolutionary algorithm for RNA folding","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2088387037","doi":"https://doi.org/10.1109/cibcb.2010.5510321","mag":"2088387037"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2010.5510321","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2010.5510321","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","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/A5049270004","display_name":"Kay C. Wiese","orcid":"https://orcid.org/0000-0003-4507-1892"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Kay C. Wiese","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Surrey, BC, Canada","[School of Computing Science, Simon Fraser University, Surrey, B.C., Canada]"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[School of Computing Science, Simon Fraser University, Surrey, B.C., Canada]","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051043145","display_name":"A. Hendriks","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Andrew G. Hendriks","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Surrey, BC, Canada","[School of Computing Science, Simon Fraser University, Surrey, B.C., Canada]"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[School of Computing Science, Simon Fraser University, Surrey, B.C., Canada]","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049270004"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":null,"apc_paid":null,"fwci":0.1322,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53407441,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"3","issue":null,"first_page":"1","last_page":"8"},"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":0.9984999895095825,"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/T10604","display_name":"RNA Research and Splicing","score":0.9915000200271606,"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/stacking","display_name":"Stacking","score":0.6430362462997437},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.6263996362686157},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5883991122245789},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5357754230499268},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.4913589060306549},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46327516436576843},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.45737385749816895},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.42842721939086914},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40783748030662537},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3719657063484192},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3286399245262146},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2632853388786316},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2562577724456787},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.21446368098258972},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16726353764533997},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10083132982254028},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09556958079338074}],"concepts":[{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.6430362462997437},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6263996362686157},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5883991122245789},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5357754230499268},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.4913589060306549},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46327516436576843},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.45737385749816895},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.42842721939086914},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40783748030662537},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3719657063484192},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3286399245262146},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2632853388786316},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2562577724456787},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.21446368098258972},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16726353764533997},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10083132982254028},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09556958079338074},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2010.5510321","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2010.5510321","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8299999833106995,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1226599","https://openalex.org/W99032621","https://openalex.org/W113288072","https://openalex.org/W1519185585","https://openalex.org/W1541914161","https://openalex.org/W1543271055","https://openalex.org/W1558375422","https://openalex.org/W1574643310","https://openalex.org/W1585306636","https://openalex.org/W1945034450","https://openalex.org/W2007799540","https://openalex.org/W2009818318","https://openalex.org/W2017965868","https://openalex.org/W2037630932","https://openalex.org/W2051713039","https://openalex.org/W2054931730","https://openalex.org/W2061949374","https://openalex.org/W2064580019","https://openalex.org/W2075702353","https://openalex.org/W2096718668","https://openalex.org/W2113368761","https://openalex.org/W2123575095","https://openalex.org/W2141157874","https://openalex.org/W2142056356","https://openalex.org/W2155544170","https://openalex.org/W2160826159","https://openalex.org/W2164943294","https://openalex.org/W2166843422","https://openalex.org/W2171582839","https://openalex.org/W2171909013","https://openalex.org/W2415556764","https://openalex.org/W6600050089","https://openalex.org/W6604038483","https://openalex.org/W6681001129"],"related_works":["https://openalex.org/W2035329725","https://openalex.org/W4376641153","https://openalex.org/W2070875936","https://openalex.org/W4250391473","https://openalex.org/W3045075405","https://openalex.org/W1945034450","https://openalex.org/W2098906711","https://openalex.org/W2064060814","https://openalex.org/W2396713240","https://openalex.org/W2904092608"],"abstract_inverted_index":{"The":[0,108],"shape":[1],"that":[2,23],"organic":[3,10],"molecules":[4,17],"such":[5],"as":[6],"biopolymers":[7],"form":[8],"within":[9],"systems":[11],"largely":[12],"determines":[13],"the":[14,43,58,81,90,127],"function":[15],"said":[16],"perform.":[18],"RNA":[19,64,76],"is":[20,71,113,123],"a":[21,25,62,67,98,116],"biopolymer":[22],"plays":[24],"central":[26],"part":[27],"in":[28,42],"several":[29],"stages":[30],"of":[31,57,61,83,111,118],"protein":[32],"synthesis,":[33],"and":[34,39,95],"also":[35,124],"has":[36],"structural,":[37],"functional,":[38],"regulatory":[40],"roles":[41],"cell.":[44],"In":[45],"an":[46,72,84],"ab":[47],"initio":[48],"case":[49],"most":[50],"common":[51],"structure":[52],"prediction":[53,109,129],"techniques":[54],"employ":[55],"minimization":[56],"free":[59],"energy":[60],"given":[63],"molecule":[65],"via":[66],"thermodynamic":[68,86,92],"model.":[69],"RnaPredict":[70],"evolutionary":[73],"algorithm":[74,130],"for":[75],"folding.":[77],"This":[78],"paper":[79],"compares":[80],"performance":[82],"advanced":[85],"model,":[87],"efn2,":[88],"against":[89],"stacking-energy":[91],"models":[93],"INN":[94],"INN-HB":[96],"on":[97,115],"test":[99,119],"set":[100],"containing":[101],"24":[102],"sequences":[103],"from":[104],"4":[105],"rRNA":[106],"subtypes.":[107],"accuracy":[110],"efn2":[112],"demonstrated":[114,132],"majority":[117],"sequences.":[120],"A":[121],"comparison":[122],"made":[125],"with":[126],"mfold":[128],"which":[131],"RnaPredict's":[133],"comparable":[134],"performance.":[135]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
