{"id":"https://openalex.org/W1945034450","doi":"https://doi.org/10.1109/cec.2004.1330912","title":"Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - a comparison to known structures","display_name":"Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - a comparison to known structures","publication_year":2004,"publication_date":"2004-09-28","ids":{"openalex":"https://openalex.org/W1945034450","doi":"https://doi.org/10.1109/cec.2004.1330912","mag":"1945034450"},"language":"en","primary_location":{"id":"doi:10.1109/cec.2004.1330912","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2004.1330912","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753)","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/A5028696560","display_name":"A. Deschenes","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":true,"raw_author_name":"A. Deschenes","raw_affiliation_strings":["InfoNet Media Center, Simon Fraser University, Surrey, BC, Canada","InfoNet Media Center, Simon Fraser Univ., Surrey, BC, Canada"],"affiliations":[{"raw_affiliation_string":"InfoNet Media Center, Simon Fraser University, Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"InfoNet Media Center, Simon Fraser Univ., Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","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":false,"raw_author_name":"K.C. Wiese","raw_affiliation_strings":["InfoNet Media Center, Simon Fraser University, Surrey, BC, Canada","InfoNet Media Center, Simon Fraser Univ., Surrey, BC, Canada"],"affiliations":[{"raw_affiliation_string":"InfoNet Media Center, Simon Fraser University, Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"InfoNet Media Center, Simon Fraser Univ., Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5028696560"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":null,"apc_paid":null,"fwci":2.105,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.86003674,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"598","last_page":"606"},"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.984499990940094,"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":0.975600004196167,"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":0.9557824730873108},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6383984088897705},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.6184341311454773},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6091347932815552},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.5911595821380615},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5726562738418579},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4621480405330658},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.45934754610061646},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3855273723602295},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38528522849082947},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3434879779815674},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3211962878704071},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3187524676322937},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2969922423362732},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2517783045768738},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2191375494003296},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.21681365370750427},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15184789896011353},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.09162327647209167}],"concepts":[{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.9557824730873108},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6383984088897705},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6184341311454773},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6091347932815552},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.5911595821380615},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5726562738418579},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4621480405330658},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.45934754610061646},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3855273723602295},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38528522849082947},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3434879779815674},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3211962878704071},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3187524676322937},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2969922423362732},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2517783045768738},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2191375494003296},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.21681365370750427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15184789896011353},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.09162327647209167},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cec.2004.1330912","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2004.1330912","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.699999988079071,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1226599","https://openalex.org/W17748033","https://openalex.org/W99032621","https://openalex.org/W1497256448","https://openalex.org/W1507363803","https://openalex.org/W1516301787","https://openalex.org/W1519185585","https://openalex.org/W1522107594","https://openalex.org/W1541914161","https://openalex.org/W1544962352","https://openalex.org/W1574643310","https://openalex.org/W1859892029","https://openalex.org/W1969744746","https://openalex.org/W1998358440","https://openalex.org/W2002164298","https://openalex.org/W2007799540","https://openalex.org/W2009818318","https://openalex.org/W2010352098","https://openalex.org/W2031211180","https://openalex.org/W2037630932","https://openalex.org/W2039509053","https://openalex.org/W2040015982","https://openalex.org/W2051713039","https://openalex.org/W2064580019","https://openalex.org/W2067822099","https://openalex.org/W2075702353","https://openalex.org/W2076756368","https://openalex.org/W2091735434","https://openalex.org/W2096590200","https://openalex.org/W2113368761","https://openalex.org/W2120624274","https://openalex.org/W2142056356","https://openalex.org/W2145149786","https://openalex.org/W2164943294","https://openalex.org/W2415556764","https://openalex.org/W2976664243","https://openalex.org/W4234886514","https://openalex.org/W4237234846","https://openalex.org/W4285719527","https://openalex.org/W6600050089","https://openalex.org/W6600690991","https://openalex.org/W6604038483","https://openalex.org/W6630399596","https://openalex.org/W6630838125","https://openalex.org/W6631287414","https://openalex.org/W6632716904"],"related_works":["https://openalex.org/W2114431227","https://openalex.org/W2006115832","https://openalex.org/W2015299906","https://openalex.org/W2026354057","https://openalex.org/W12856195","https://openalex.org/W1633574359","https://openalex.org/W2078871596","https://openalex.org/W2143726250","https://openalex.org/W4385948849","https://openalex.org/W4295093566"],"abstract_inverted_index":{"This":[0],"paper":[1],"builds":[2],"on":[3,42,75],"previous":[4],"research":[5],"from":[6],"an":[7],"EA":[8,18,111],"used":[9],"to":[10,45,92,109],"predict":[11],"secondary":[12],"structure":[13,104],"of":[14,68,79,86,100],"RNA":[15,66],"molecules.":[16],"The":[17,39,51,84],"predicts":[19],"which":[20],"specific":[21],"canonical":[22],"base":[23,48,60],"pairs":[24],"forms":[25],"hydrogen":[26],"bonds":[27],"and":[28,55,72,81],"helices.":[29],"Three":[30],"new":[31],"thermodynamic":[32],"models":[33],"were":[34],"integrated":[35],"into":[36],"our":[37,46,110],"EA.":[38],"first":[40],"based":[41],"a":[43,76],"modification":[44],"original":[47],"pair":[49,61],"model.":[50],"last":[52],"two,":[53],"INN":[54],"INN-HB,":[56],"add":[57],"stacking-energies":[58,102],"using":[59,101],"adjacencies.":[62],"We":[63],"have":[64],"tested":[65],"sequences":[67],"lengths":[69],"122,":[70],"543,":[71],"1494":[73],"nucleotides":[74],"wide":[77],"variety":[78],"operators":[80],"parameters":[82],"settings.":[83],"accuracy":[85],"the":[87,93,98],"predicted":[88],"structures":[89,95],"is":[90],"compared":[91],"known":[94],"thus":[96],"demonstrating":[97],"benefits":[99],"in":[103],"prediction.":[105],"Some":[106],"other":[107],"improvements":[108],"are":[112],"also":[113],"discussed.":[114]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}