{"id":"https://openalex.org/W4403826568","doi":"https://doi.org/10.1371/journal.pcbi.1012293","title":"IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation","display_name":"IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation","publication_year":2024,"publication_date":"2024-10-28","ids":{"openalex":"https://openalex.org/W4403826568","doi":"https://doi.org/10.1371/journal.pcbi.1012293","pmid":"https://pubmed.ncbi.nlm.nih.gov/39466881"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012293","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012293","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012293","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101349371","display_name":"Haolin Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haolin Jiang","raw_affiliation_strings":["College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I4210098931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101911394","display_name":"Yulian Xu","orcid":"https://orcid.org/0000-0003-0608-544X"},"institutions":[{"id":"https://openalex.org/I55538621","display_name":"China Jiliang University","ror":"https://ror.org/05v1y0t93","country_code":"CN","type":"education","lineage":["https://openalex.org/I55538621"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yulian Xu","raw_affiliation_strings":["China Jiliang University-Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, China","College of Life Sciences, China Jiliang University, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"China Jiliang University-Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, China","institution_ids":["https://openalex.org/I55538621"]},{"raw_affiliation_string":"College of Life Sciences, China Jiliang University, Hangzhou, China","institution_ids":["https://openalex.org/I55538621"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102121960","display_name":"Yunguang Tong","orcid":null},"institutions":[{"id":"https://openalex.org/I4210142178","display_name":"Hangzhou DAC Biotech (China)","ror":"https://ror.org/04hy71c73","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210142178"]},{"id":"https://openalex.org/I55538621","display_name":"China Jiliang University","ror":"https://ror.org/05v1y0t93","country_code":"CN","type":"education","lineage":["https://openalex.org/I55538621"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunguang Tong","raw_affiliation_strings":["Aoming (Hangzhou) Biomedical Co., Ltd., Hangzhou, China","College of Life Sciences, China Jiliang University, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aoming (Hangzhou) Biomedical Co., Ltd., Hangzhou, China","institution_ids":["https://openalex.org/I4210142178"]},{"raw_affiliation_string":"College of Life Sciences, China Jiliang University, Hangzhou, China","institution_ids":["https://openalex.org/I55538621"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004328556","display_name":"Dong Zhang","orcid":"https://orcid.org/0000-0001-7297-5083"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Zhang","raw_affiliation_strings":["College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China"],"raw_orcid":"https://orcid.org/0000-0001-7297-5083","affiliations":[{"raw_affiliation_string":"College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I4210098931"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078014032","display_name":"Ruhong Zhou","orcid":"https://orcid.org/0000-0001-8624-5591"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Ruhong Zhou","raw_affiliation_strings":["College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China","The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6123,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.68662563,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"20","issue":"10","first_page":"e1012293","last_page":"e1012293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","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"}},"topics":[{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","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":0.9927999973297119,"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":0.9922999739646912,"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":0.6278335452079773},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5625909566879272},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5559508800506592},{"id":"https://openalex.org/keywords/circular-rna","display_name":"Circular RNA","score":0.5319718718528748},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.4788605868816376},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4587221145629883},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4489825367927551},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.44837674498558044},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.4404337704181671},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4033081829547882},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3807254731655121},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24396473169326782},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22919857501983643},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12645503878593445}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6278335452079773},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5625909566879272},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5559508800506592},{"id":"https://openalex.org/C2775893923","wikidata":"https://www.wikidata.org/wiki/Q17113455","display_name":"Circular RNA","level":4,"score":0.5319718718528748},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.4788605868816376},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4587221145629883},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4489825367927551},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.44837674498558044},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.4404337704181671},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4033081829547882},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3807254731655121},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24396473169326782},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22919857501983643},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12645503878593445},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1012293","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012293","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:39466881","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39466881","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11542809","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11542809","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542809/pdf/pcbi.1012293.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1012293","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012293","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:23c098fb03f64df8bf41d2d31c5cfe6d","is_oa":true,"landing_page_url":"https://doaj.org/article/23c098fb03f64df8bf41d2d31c5cfe6d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 10, p e1012293 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012293","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012293","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2228442085","display_name":null,"funder_award_id":"U1967217","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G412652938","display_name":null,"funder_award_id":"12104396","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5878354135","display_name":null,"funder_award_id":"2021YFA1201200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8239521741","display_name":null,"funder_award_id":"2021YFF1200404","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1933156045","https://openalex.org/W1966411071","https://openalex.org/W1976961172","https://openalex.org/W1995164506","https://openalex.org/W2019465613","https://openalex.org/W2031593782","https://openalex.org/W2055493067","https://openalex.org/W2058835062","https://openalex.org/W2080284797","https://openalex.org/W2103894153","https://openalex.org/W2106434056","https://openalex.org/W2128549339","https://openalex.org/W2135300233","https://openalex.org/W2141458291","https://openalex.org/W2142739728","https://openalex.org/W2152719653","https://openalex.org/W2167564948","https://openalex.org/W2175514210","https://openalex.org/W2303457541","https://openalex.org/W2316171452","https://openalex.org/W2341963847","https://openalex.org/W2473991067","https://openalex.org/W2615136515","https://openalex.org/W2791622405","https://openalex.org/W2904657261","https://openalex.org/W2942134847","https://openalex.org/W2943205517","https://openalex.org/W2981760759","https://openalex.org/W3082572947","https://openalex.org/W3126546267","https://openalex.org/W3210418329","https://openalex.org/W3213615006","https://openalex.org/W4205718783","https://openalex.org/W4283585788","https://openalex.org/W4283832815","https://openalex.org/W4320920910","https://openalex.org/W4386804219","https://openalex.org/W4388946853"],"related_works":["https://openalex.org/W2017993626","https://openalex.org/W4320486808","https://openalex.org/W2018280025","https://openalex.org/W2101246922","https://openalex.org/W4401628082","https://openalex.org/W2080192212","https://openalex.org/W4322623665","https://openalex.org/W3128279840","https://openalex.org/W2516827041","https://openalex.org/W2097168352"],"abstract_inverted_index":{"As":[0],"an":[1,64],"emerging":[2],"class":[3],"of":[4,28,38,58,66,87,90,174],"RNA":[5,43,76],"molecules,":[6],"circular":[7,42,59,75,116,138,175],"RNAs":[8],"play":[9],"pivotal":[10],"roles":[11],"in":[12,126],"various":[13],"biological":[14,30],"processes,":[15],"thereby":[16],"determining":[17],"their":[18,29],"three-dimensional":[19],"(3D)":[20],"structure":[21,45,78,99,113],"is":[22,47,161],"crucial":[23],"for":[24,41,115,131],"a":[25,132,162],"deep":[26],"understanding":[27],"significances.":[31],"Similar":[32],"to":[33,73,165],"linear":[34],"RNAs,":[35,117,139],"the":[36,51,121,127,150,167],"development":[37],"computational":[39],"methods":[40],"3D":[44,77,112,144],"prediction":[46],"challenging,":[48],"especially":[49],"considering":[50],"inherent":[52],"flexibility":[53],"and":[54,101],"potentially":[55],"long":[56],"length":[57],"RNAs.":[60,176],"Here,":[61],"we":[62],"introduce":[63],"extension":[65],"our":[67,140,158],"previous":[68],"IsRNA2":[69],"model,":[70],"named":[71],"IsRNAcirc,":[72],"enable":[74],"predictions":[79,114],"through":[80],"coarse-grained":[81],"molecular":[82],"dynamics":[83],"simulations.":[84],"The":[85],"workflow":[86],"IsRNAcirc":[88,108,141,159],"consists":[89],"four":[91],"main":[92],"steps,":[93],"including":[94],"input":[95],"preparation,":[96],"end":[97],"closure,":[98],"prediction,":[100],"model":[102],"refinement.":[103],"Our":[104],"results":[105],"demonstrate":[106,156],"that":[107,157],"can":[109,142],"provide":[110],"reasonable":[111],"which":[118],"significantly":[119],"reduce":[120],"locally":[122],"irrational":[123],"elements":[124],"contained":[125],"initial":[128],"input.":[129],"Moreover,":[130],"validation":[133],"test":[134],"set":[135],"comprising":[136],"34":[137],"generate":[143],"models":[145],"with":[146,171],"better":[147],"scores":[148],"than":[149],"template-based":[151],"3dRNA":[152],"method.":[153],"These":[154],"findings":[155],"method":[160],"promising":[163],"tool":[164],"explore":[166],"structural":[168],"details":[169],"along":[170],"intricate":[172],"interactions":[173]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}