{"id":"https://openalex.org/W4399474256","doi":"https://doi.org/10.1093/gpbjnl/qzae043","title":"Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes","display_name":"Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399474256","doi":"https://doi.org/10.1093/gpbjnl/qzae043","pmid":"https://pubmed.ncbi.nlm.nih.gov/39317944"},"language":"en","primary_location":{"id":"doi:10.1093/gpbjnl/qzae043","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzae043","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzae043/58177451/qzae043.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzae043/58177451/qzae043.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005245031","display_name":"Fei Qi","orcid":"https://orcid.org/0000-0003-4578-0146"},"institutions":[{"id":"https://openalex.org/I119045251","display_name":"Huaqiao University","ror":"https://ror.org/03frdh605","country_code":"CN","type":"education","lineage":["https://openalex.org/I119045251"]},{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fei Qi","raw_affiliation_strings":["Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University , Xiamen 361102,","Xiamen University State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, , Xiamen 361102, China","Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China"],"affiliations":[{"raw_affiliation_string":"Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","institution_ids":["https://openalex.org/I119045251"]},{"raw_affiliation_string":"State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University , Xiamen 361102,","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen University State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, , Xiamen 361102, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China","institution_ids":["https://openalex.org/I119045251"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007230921","display_name":"Junjie Chen","orcid":"https://orcid.org/0000-0003-3386-5759"},"institutions":[{"id":"https://openalex.org/I119045251","display_name":"Huaqiao University","ror":"https://ror.org/03frdh605","country_code":"CN","type":"education","lineage":["https://openalex.org/I119045251"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junjie Chen","raw_affiliation_strings":["Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China"],"affiliations":[{"raw_affiliation_string":"Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","institution_ids":["https://openalex.org/I119045251"]},{"raw_affiliation_string":"Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China","institution_ids":["https://openalex.org/I119045251"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068179207","display_name":"Yue Chen","orcid":"https://orcid.org/0000-0002-1799-6647"},"institutions":[{"id":"https://openalex.org/I119045251","display_name":"Huaqiao University","ror":"https://ror.org/03frdh605","country_code":"CN","type":"education","lineage":["https://openalex.org/I119045251"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yue Chen","raw_affiliation_strings":["Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China"],"affiliations":[{"raw_affiliation_string":"Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","institution_ids":["https://openalex.org/I119045251"]},{"raw_affiliation_string":"Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China","institution_ids":["https://openalex.org/I119045251"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078691732","display_name":"Jianfeng Sun","orcid":"https://orcid.org/0000-0002-1274-5080"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146357","display_name":"Oxford BioMedica (United Kingdom)","ror":"https://ror.org/03dp0vf82","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210146357"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jianfeng Sun","raw_affiliation_strings":["Botnar Research Centre, University of Oxford , Oxford, OX3 7LD,","University of Oxford Botnar Research Centre, , Oxford OX3 7LD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Botnar Research Centre, University of Oxford , Oxford, OX3 7LD,","institution_ids":["https://openalex.org/I4210146357","https://openalex.org/I40120149"]},{"raw_affiliation_string":"University of Oxford Botnar Research Centre, , Oxford OX3 7LD, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101980127","display_name":"Yiting Lin","orcid":"https://orcid.org/0000-0001-8014-0449"},"institutions":[{"id":"https://openalex.org/I119045251","display_name":"Huaqiao University","ror":"https://ror.org/03frdh605","country_code":"CN","type":"education","lineage":["https://openalex.org/I119045251"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiting Lin","raw_affiliation_strings":["Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China"],"affiliations":[{"raw_affiliation_string":"Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","institution_ids":["https://openalex.org/I119045251"]},{"raw_affiliation_string":"Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China","institution_ids":["https://openalex.org/I119045251"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034983157","display_name":"Zipeng Chen","orcid":"https://orcid.org/0000-0002-8257-3165"},"institutions":[{"id":"https://openalex.org/I119045251","display_name":"Huaqiao University","ror":"https://ror.org/03frdh605","country_code":"CN","type":"education","lineage":["https://openalex.org/I119045251"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zipeng Chen","raw_affiliation_strings":["Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China"],"affiliations":[{"raw_affiliation_string":"Institute of Genomics, School of Medicine, Huaqiao University , Xiamen 361021,","institution_ids":["https://openalex.org/I119045251"]},{"raw_affiliation_string":"Huaqiao University Institute of Genomics, School of Medicine, , Xiamen 361021, China","institution_ids":["https://openalex.org/I119045251"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008738173","display_name":"Philipp Kapranov","orcid":"https://orcid.org/0000-0003-2647-4856"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Philipp Kapranov","raw_affiliation_strings":["State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University , Xiamen 361102,","Xiamen University State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, , Xiamen 361102, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University , Xiamen 361102,","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Xiamen University State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, , Xiamen 361102, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5005245031"],"corresponding_institution_ids":["https://openalex.org/I119045251","https://openalex.org/I191208505"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":0.6843,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.68564193,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"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":0.9997000098228455,"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":0.9961000084877014,"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/ribozyme","display_name":"Ribozyme","score":0.945257306098938},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6299129128456116},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5096039772033691},{"id":"https://openalex.org/keywords/ligase-ribozyme","display_name":"Ligase ribozyme","score":0.5001976490020752},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4606625437736511},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.34067368507385254},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2460583746433258},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12551864981651306},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08359575271606445}],"concepts":[{"id":"https://openalex.org/C76346623","wikidata":"https://www.wikidata.org/wiki/Q205858","display_name":"Ribozyme","level":4,"score":0.945257306098938},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6299129128456116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5096039772033691},{"id":"https://openalex.org/C1342335","wikidata":"https://www.wikidata.org/wiki/Q6545871","display_name":"Ligase ribozyme","level":5,"score":0.5001976490020752},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4606625437736511},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34067368507385254},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2460583746433258},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12551864981651306},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08359575271606445}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"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":"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},{"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":4,"locations":[{"id":"doi:10.1093/gpbjnl/qzae043","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzae043","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzae043/58177451/qzae043.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39317944","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39317944","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12016570","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12016570","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12016570/pdf/qzae043.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genomics Proteomics Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:8f48b7cf-0524-4c85-91aa-43127b2d1e5d","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jisc Publications Router","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/gpbjnl/qzae043","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzae043","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzae043/58177451/qzae043.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G10161780","display_name":null,"funder_award_id":"2020J02006","funder_id":"https://openalex.org/F4320321878","funder_display_name":"Natural Science Foundation of Fujian Province"},{"id":"https://openalex.org/G1147688885","display_name":null,"funder_award_id":"32000462","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2025695628","display_name":null,"funder_award_id":"32201055","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2981938667","display_name":null,"funder_award_id":"Shenzhen","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3085993365","display_name":null,"funder_award_id":"(Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5498277196","display_name":null,"funder_award_id":"21507105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6072478317","display_name":null,"funder_award_id":"201055","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G652446290","display_name":null,"funder_award_id":"32150710525","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7523835264","display_name":null,"funder_award_id":"32170619","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321878","display_name":"Natural Science Foundation of Fujian Province","ror":null},{"id":"https://openalex.org/F4320322182","display_name":"Huaqiao University","ror":"https://ror.org/03frdh605"},{"id":"https://openalex.org/F4320331248","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4399474256.pdf"},"referenced_works_count":85,"referenced_works":["https://openalex.org/W1481166764","https://openalex.org/W1585990551","https://openalex.org/W1881326155","https://openalex.org/W1964607399","https://openalex.org/W1985278607","https://openalex.org/W1994958501","https://openalex.org/W2005650685","https://openalex.org/W2006247279","https://openalex.org/W2007423986","https://openalex.org/W2007550449","https://openalex.org/W2021333801","https://openalex.org/W2022199909","https://openalex.org/W2037367916","https://openalex.org/W2041882488","https://openalex.org/W2041985017","https://openalex.org/W2054613021","https://openalex.org/W2060535588","https://openalex.org/W2063336974","https://openalex.org/W2069165607","https://openalex.org/W2074882547","https://openalex.org/W2083543262","https://openalex.org/W2086561953","https://openalex.org/W2095520518","https://openalex.org/W2097654784","https://openalex.org/W2098553089","https://openalex.org/W2106293441","https://openalex.org/W2109389103","https://openalex.org/W2109553965","https://openalex.org/W2110304798","https://openalex.org/W2119336718","https://openalex.org/W2129193172","https://openalex.org/W2131462431","https://openalex.org/W2132046933","https://openalex.org/W2134489577","https://openalex.org/W2141157874","https://openalex.org/W2141351700","https://openalex.org/W2143393352","https://openalex.org/W2143407915","https://openalex.org/W2144546818","https://openalex.org/W2145476823","https://openalex.org/W2147253833","https://openalex.org/W2155944730","https://openalex.org/W2159946246","https://openalex.org/W2162029177","https://openalex.org/W2167470206","https://openalex.org/W2181035467","https://openalex.org/W2196304378","https://openalex.org/W2237727050","https://openalex.org/W2489381017","https://openalex.org/W2502239405","https://openalex.org/W2571083978","https://openalex.org/W2591974314","https://openalex.org/W2762224301","https://openalex.org/W2767146376","https://openalex.org/W2785449688","https://openalex.org/W2807635396","https://openalex.org/W2808896479","https://openalex.org/W2970786047","https://openalex.org/W2982232056","https://openalex.org/W2990528340","https://openalex.org/W2998627042","https://openalex.org/W3048927351","https://openalex.org/W3049756659","https://openalex.org/W3087202564","https://openalex.org/W3095370870","https://openalex.org/W3126773939","https://openalex.org/W3135161193","https://openalex.org/W3136001083","https://openalex.org/W3136740038","https://openalex.org/W3147095886","https://openalex.org/W3157907911","https://openalex.org/W3160029886","https://openalex.org/W3177828909","https://openalex.org/W3185894165","https://openalex.org/W3194959410","https://openalex.org/W3195820203","https://openalex.org/W3204096889","https://openalex.org/W3212533323","https://openalex.org/W4220832915","https://openalex.org/W4237038552","https://openalex.org/W4282945580","https://openalex.org/W4313488537","https://openalex.org/W4393734376","https://openalex.org/W6731597378","https://openalex.org/W6785246590"],"related_works":["https://openalex.org/W2110871443","https://openalex.org/W4246691542","https://openalex.org/W1982338359","https://openalex.org/W2420157817","https://openalex.org/W71028484","https://openalex.org/W3187151242","https://openalex.org/W4206214605","https://openalex.org/W4210374766","https://openalex.org/W1996962471","https://openalex.org/W4311648110"],"abstract_inverted_index":{"Accurate":[0],"identification":[1],"of":[2,15,27,30,45,79,82,95,106,114,133,135,140,142,156,210,220],"the":[3,22,25,80,104,131,190,194,199,207,218],"correct,":[4],"biologically":[5,136],"relevant":[6,137],"RNA":[7,16,31,55,118,150,178,200,221],"structures":[8,56,139],"is":[9],"critical":[10],"to":[11,24,50,110],"understanding":[12],"various":[13,59],"aspects":[14],"biology":[17],"since":[18],"proper":[19],"folding":[20,151,179],"represents":[21],"key":[23],"functionality":[26],"all":[28,74],"types":[29],"molecules":[32],"and":[33,87],"plays":[34],"pivotal":[35],"roles":[36],"in":[37,77,93,116,148,167,175,182,193,197],"many":[38,163],"essential":[39],"biological":[40],"processes.":[41],"Thus,":[42],"a":[43,111,184],"plethora":[44],"approaches":[46,69,122],"have":[47],"been":[48],"developed":[49],"predict,":[51],"identify,":[52],"or":[53,64],"solve":[54],"based":[57,205],"on":[58,206],"computational,":[60],"molecular,":[61],"genetic,":[62],"chemical,":[63],"physicochemical":[65],"strategies.":[66],"Purely":[67],"computational":[68],"hold":[70],"distinct":[71],"advantages":[72,105],"over":[73],"other":[75,191],"strategies":[76],"terms":[78,94],"ease":[81],"implementation,":[83],"time,":[84],"speed,":[85],"cost,":[86],"throughput,":[88],"but":[89],"they":[90],"strongly":[91],"underperform":[92],"accuracy":[96,132],"that":[97,161,214],"significantly":[98,174],"limits":[99],"their":[100,171],"broader":[101],"application.":[102],"Nonetheless,":[103],"these":[107],"methods":[108],"led":[109],"steady":[112],"development":[113],"multiple":[115],"silico":[117,149],"secondary":[119,138,201],"structure":[120,222],"prediction":[121,152,223],"including":[123],"recent":[124],"deep":[125,186],"learning-based":[126],"programs.":[127],"Here,":[128],"we":[129],"compared":[130],"predictions":[134],"dozens":[141],"self-cleaving":[143],"ribozyme":[144],"sequences":[145,211],"using":[146],"seven":[147],"tools":[153],"with":[154],"tasks":[155,196],"varying":[157],"complexity.":[158],"We":[159],"found":[160],"while":[162],"programs":[164,192],"performed":[165],"well":[166],"relatively":[168],"simple":[169],"tasks,":[170],"performance":[172],"varied":[173],"more":[176],"complex":[177,195],"problems.":[180],"However,":[181],"general,":[183],"modern":[185],"learning":[187],"method":[188],"outperformed":[189],"predicting":[198],"structures,":[202],"at":[203],"least":[204],"specific":[208],"class":[209],"tested,":[212],"suggesting":[213],"it":[215],"may":[216],"represent":[217],"future":[219],"algorithms.":[224]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
