{"id":"https://openalex.org/W2136295476","doi":"https://doi.org/10.1093/bioinformatics/btv221","title":"iFoldRNA v2: folding RNA with constraints","display_name":"iFoldRNA v2: folding RNA with constraints","publication_year":2015,"publication_date":"2015-04-24","ids":{"openalex":"https://openalex.org/W2136295476","doi":"https://doi.org/10.1093/bioinformatics/btv221","mag":"2136295476","pmid":"https://pubmed.ncbi.nlm.nih.gov/25910700"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv221","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/17/2891/49034850/bioinformatics_31_17_2891.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/17/2891/49034850/bioinformatics_31_17_2891.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5105657677","display_name":"A. Krokhotin","orcid":"https://orcid.org/0009-0006-4435-3213"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrey Krokhotin","raw_affiliation_strings":["Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036475340","display_name":"Kevin Houlihan","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Houlihan","raw_affiliation_strings":["Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033490428","display_name":"Nikolay V. Dokholyan","orcid":"https://orcid.org/0000-0002-8225-4025"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikolay V. Dokholyan","raw_affiliation_strings":["Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.0666,"has_fulltext":true,"cited_by_count":138,"citation_normalized_percentile":{"value":0.94554946,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"31","issue":"17","first_page":"2891","last_page":"2893"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9728999733924866,"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":0.9728999733924866,"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":0.011699999682605267,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00419999985024333,"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/rna","display_name":"RNA","score":0.7727025747299194},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6374621987342834},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.6002984046936035},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5623002052307129},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.5451175570487976},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4942479431629181},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4705921411514282},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.45206934213638306},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.45013418793678284},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.431145578622818},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.42583000659942627},{"id":"https://openalex.org/keywords/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.4155055582523346},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3326687216758728},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3255731463432312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27649402618408203},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1521870493888855},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13148358464241028},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12123352289199829},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1162242591381073},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09741443395614624},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08501973748207092}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7727025747299194},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6374621987342834},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.6002984046936035},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5623002052307129},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.5451175570487976},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4942479431629181},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4705921411514282},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.45206934213638306},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.45013418793678284},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.431145578622818},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.42583000659942627},{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.4155055582523346},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3326687216758728},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3255731463432312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27649402618408203},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1521870493888855},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13148358464241028},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12123352289199829},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1162242591381073},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09741443395614624},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08501973748207092},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017665","descriptor_name":"Hydroxyl Radical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017665","descriptor_name":"Hydroxyl Radical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017665","descriptor_name":"Hydroxyl Radical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv221","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/17/2891/49034850/bioinformatics_31_17_2891.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25910700","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25910700","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4547609","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4547609","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/17/2891","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/17/2891","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv221","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv221","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/17/2891/49034850/bioinformatics_31_17_2891.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5699999928474426,"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth"}],"awards":[{"id":"https://openalex.org/G7052867482","display_name":null,"funder_award_id":"GM064803","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136295476.pdf","grobid_xml":"https://content.openalex.org/works/W2136295476.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1995717154","https://openalex.org/W2009698138","https://openalex.org/W2036412199","https://openalex.org/W2040809566","https://openalex.org/W2053150979","https://openalex.org/W2077064224","https://openalex.org/W2106434056","https://openalex.org/W2109987496","https://openalex.org/W2118780761","https://openalex.org/W2119896557","https://openalex.org/W2151538750","https://openalex.org/W2157467256","https://openalex.org/W2158073100","https://openalex.org/W2170196847","https://openalex.org/W2171706075"],"related_works":["https://openalex.org/W2096976538","https://openalex.org/W2119881887","https://openalex.org/W4386361828","https://openalex.org/W576226539","https://openalex.org/W2097627156","https://openalex.org/W2808896479","https://openalex.org/W2133070749","https://openalex.org/W1978187259","https://openalex.org/W1551265320","https://openalex.org/W2061103938"],"abstract_inverted_index":{"UNLABELLED:":[0],"A":[1],"key":[2],"to":[3,8],"understanding":[4],"RNA":[5,19,53],"function":[6],"is":[7,92],"uncover":[9],"its":[10],"complex":[11],"3D":[12,20],"structure.":[13],"Experimental":[14],"methods":[15,34],"used":[16],"for":[17],"determining":[18],"structures":[21,54],"are":[22],"technologically":[23],"challenging":[24],"and":[25,102,116],"laborious,":[26],"which":[27],"makes":[28],"the":[29,41,66,71,89],"development":[30],"of":[31,35,48,65,73,76,96,113],"computational":[32,117],"prediction":[33,47,72],"substantial":[36,86],"interest.":[37],"Previously,":[38],"we":[39,60],"developed":[40],"iFoldRNA":[42,67],"server":[43,68,90],"that":[44,69],"allows":[45],"accurate":[46],"short":[49],"(<50":[50],"nt)":[51],"tertiary":[52,74],"starting":[55],"from":[56],"primary":[57],"sequences.":[58],"Here,":[59],"present":[61],"a":[62,81,107],"new":[63],"version":[64],"permits":[70],"structure":[75],"RNAs":[77],"as":[78,80,100],"long":[79],"few":[82],"hundred":[83],"nucleotides.":[84],"This":[85],"increase":[87],"in":[88],"capacity":[91],"achieved":[93],"by":[94,111],"utilization":[95],"experimental":[97,114],"information":[98],"such":[99],"base-pairing":[101],"hydroxyl-radical":[103],"probing.":[104],"We":[105],"demonstrate":[106],"significant":[108],"benefit":[109],"provided":[110],"integration":[112],"data":[115],"methods.":[118],"AVAILABILITY":[119],"AND":[120],"IMPLEMENTATION:":[121],"http://ifoldrna.dokhlab.org":[122],"CONTACT:":[123],"dokh@unc.eu.":[124]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
