{"id":"https://openalex.org/W2089019240","doi":"https://doi.org/10.1186/s12859-014-0444-5","title":"ERD: a fast and reliable tool for RNA design including constraints","display_name":"ERD: a fast and reliable tool for RNA design including constraints","publication_year":2015,"publication_date":"2015-01-27","ids":{"openalex":"https://openalex.org/W2089019240","doi":"https://doi.org/10.1186/s12859-014-0444-5","mag":"2089019240","pmid":"https://pubmed.ncbi.nlm.nih.gov/25626878"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-014-0444-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0444-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0444-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0444-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010477043","display_name":"Ali Esmaili-Taheri","orcid":null},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Ali Esmaili-Taheri","raw_affiliation_strings":["Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran. aliesmaili@ut.ac.ir","Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science University of Tehran  Tehran Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran. aliesmaili@ut.ac.ir","institution_ids":["https://openalex.org/I23946033"]},{"raw_affiliation_string":"Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science University of Tehran  Tehran Iran","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052221301","display_name":"\u200eMohammad Ganjtabesh","orcid":"https://orcid.org/0000-0001-8062-8794"},"institutions":[{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR","IR"],"is_corresponding":true,"raw_author_name":"Mohammad Ganjtabesh","raw_affiliation_strings":["Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran. mgtabesh@ut.ac.ir","Laboratoire d'Informatique (LIX), Ecole Polytechnique, Palaiseau CEDEX, 91128, France. mgtabesh@ut.ac.ir","Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran","Laboratoire d\u2019Informatique (LIX), Ecole Polytechnique, Palaiseau CEDEX, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran. mgtabesh@ut.ac.ir","institution_ids":["https://openalex.org/I23946033"]},{"raw_affiliation_string":"Laboratoire d'Informatique (LIX), Ecole Polytechnique, Palaiseau CEDEX, 91128, France. mgtabesh@ut.ac.ir","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I4210139461"]},{"raw_affiliation_string":"Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran","institution_ids":["https://openalex.org/I23946033"]},{"raw_affiliation_string":"Laboratoire d\u2019Informatique (LIX), Ecole Polytechnique, Palaiseau CEDEX, France","institution_ids":["https://openalex.org/I142476485"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052221301"],"corresponding_institution_ids":["https://openalex.org/I142476485","https://openalex.org/I23946033","https://openalex.org/I4210139461"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":1.0935,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.76632818,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"1","first_page":"20","last_page":"20"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.973800003528595,"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":0.973800003528595,"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":0.012000000104308128,"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/T11445","display_name":"Origins and Evolution of Life","score":0.002899999963119626,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.8037346601486206},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.576937735080719},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.576873242855072},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5465904474258423},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5354288816452026},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5293874144554138},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49416616559028625},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4860280156135559},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.45462822914123535},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4525248408317566},{"id":"https://openalex.org/keywords/thermodynamic-free-energy","display_name":"Thermodynamic free energy","score":0.43794625997543335},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33993035554885864},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2718527317047119},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2574898600578308},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25290119647979736},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14782476425170898},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1219475269317627}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.8037346601486206},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.576937735080719},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.576873242855072},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5465904474258423},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5354288816452026},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5293874144554138},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49416616559028625},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4860280156135559},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.45462822914123535},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4525248408317566},{"id":"https://openalex.org/C170623327","wikidata":"https://www.wikidata.org/wiki/Q1146448","display_name":"Thermodynamic free energy","level":2,"score":0.43794625997543335},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33993035554885864},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2718527317047119},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2574898600578308},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25290119647979736},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14782476425170898},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1219475269317627},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-014-0444-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0444-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0444-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25626878","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25626878","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:3349787","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4384295","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-014-0444-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0444-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0444-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8999999761581421}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2089019240.pdf","grobid_xml":"https://content.openalex.org/works/W2089019240.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W53750313","https://openalex.org/W1543796220","https://openalex.org/W1583837637","https://openalex.org/W1860906034","https://openalex.org/W1969390039","https://openalex.org/W1996423252","https://openalex.org/W2003004847","https://openalex.org/W2006402229","https://openalex.org/W2009818318","https://openalex.org/W2012593394","https://openalex.org/W2013195357","https://openalex.org/W2013805110","https://openalex.org/W2016971241","https://openalex.org/W2038922801","https://openalex.org/W2055681612","https://openalex.org/W2057568625","https://openalex.org/W2063594852","https://openalex.org/W2072727852","https://openalex.org/W2074231493","https://openalex.org/W2081630359","https://openalex.org/W2095258877","https://openalex.org/W2096183596","https://openalex.org/W2109881896","https://openalex.org/W2111342151","https://openalex.org/W2117869369","https://openalex.org/W2122944508","https://openalex.org/W2125615424","https://openalex.org/W2135373808","https://openalex.org/W2136346399","https://openalex.org/W2140505514","https://openalex.org/W2143407915","https://openalex.org/W2152678443","https://openalex.org/W2184107140","https://openalex.org/W2913668833","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W1640318440","https://openalex.org/W2264054990","https://openalex.org/W2581888268","https://openalex.org/W2954917112","https://openalex.org/W2581348958","https://openalex.org/W4385457841"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,15,217,261,277],"function":[2,27],"of":[3,18,36,58,70,92,111,137,174,191,230],"an":[4,78,184],"RNA":[5,19,53,66,72,79,93,125,142,211,241,246],"in":[6,21,42,105,120,228,248],"cellular":[7,43],"processes":[8],"is":[9,61,75,114,117],"directly":[10],"related":[11],"to":[12,25,46,76,150,166,171,238,257,273],"its":[13,26],"structure.":[14,86],"free":[16,37,59,112,188],"energy":[17,38,60,100,113,155,179,189],"structure":[20,54],"another":[22],"important":[23],"key":[24],"as":[28],"only":[29],"some":[30,97,152,207],"structures":[31,213],"with":[32,55,199],"a":[33,48,51,64,134,167,172],"specific":[34,49,56],"level":[35,57,110],"can":[39,162,182],"take":[40],"part":[41],"reactions.":[44],"Therefore,":[45],"perform":[47],"function,":[50],"particular":[52],"required.":[62],"For":[63],"given":[65,85],"structure,":[67],"the":[68,71,84,89,109,121,158,178,187,192,224,239,244,258,274],"goal":[69],"design":[73,77,126,143],"problem":[74],"sequence":[80,98,153,159,164],"that":[81,220],"folds":[82],"into":[83],"To":[87],"mimic":[88],"biological":[90],"features":[91],"sequences":[94,247,263],"and":[95,99,147,154,203,209,214,236,255,267,280],"structures,":[96],"constraints":[101],"should":[102],"be":[103],"considered":[104,119],"designing":[106],"RNA.":[107],"Although":[108],"important,":[115],"it":[116,149],"not":[118],"available":[122,285],"approaches":[123,205,227],"for":[124,141,177,186,206],"problem.":[127],"RESULTS:":[128],"In":[129,157],"this":[130],"paper,":[131],"we":[132],"present":[133],"new":[135],"version":[136],"our":[138,197,221,249],"evolutionary":[139],"algorithm":[140,198,222],"problem,":[144],"entitled":[145],"ERD,":[146],"extend":[148],"handle":[151],"constraints.":[156,215],"constraints,":[160],"one":[161,181],"restrict":[163],"positions":[165],"fixed":[168],"nucleotide":[169],"or":[170],"subset":[173],"nucleotides.":[175],"As":[176],"constraint,":[180],"specify":[183],"interval":[185],"ranges":[190],"designed":[193,245],"sequences.":[194,242],"We":[195],"compare":[196],"INFO-RNA,":[200],"MODENA,":[201],"NUPACK,":[202],"RNAiFold":[204],"artificial":[208],"natural":[210,240,259,275],"secondary":[212],"CONCLUSIONS:":[216],"results":[218],"indicate":[219],"outperforms":[223],"other":[225],"mentioned":[226],"terms":[229],"accuracy,":[231],"speedup,":[232],"divergency,":[233],"nucleotides":[234,271],"distribution,":[235],"similarity":[237],"Particularly,":[243],"method":[250],"are":[251,264,283],"much":[252],"more":[253,265],"reliable":[254],"similar":[256],"counterparts.":[260],"generated":[262],"diverse":[266],"they":[268],"have":[269],"closer":[270],"distribution":[272],"one.":[276],"ERD":[278],"tool":[279],"web":[281],"server":[282],"freely":[284],"at":[286],"http://mostafa.ut.ac.ir/corna/erd-cons/":[287],".":[288]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-24T07:32:12.397491","created_date":"2025-10-10T00:00:00"}
