{"id":"https://openalex.org/W2941779667","doi":"https://doi.org/10.1093/bioinformatics/btz282","title":"RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA","display_name":"RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA","publication_year":2019,"publication_date":"2019-04-18","ids":{"openalex":"https://openalex.org/W2941779667","doi":"https://doi.org/10.1093/bioinformatics/btz282","mag":"2941779667","pmid":"https://pubmed.ncbi.nlm.nih.gov/31161212"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4459/30330744/btz282.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/35/21/4459/30330744/btz282.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101470197","display_name":"Sha Gong","orcid":"https://orcid.org/0000-0001-7044-4668"},"institutions":[{"id":"https://openalex.org/I10011244","display_name":"Huanggang Normal University","ror":"https://ror.org/007gf6e19","country_code":"CN","type":"education","lineage":["https://openalex.org/I10011244"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Sha Gong","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA","School of Physics and Electronic Information, Huanggang Normal University , Huanggang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I4210114445"]},{"raw_affiliation_string":"School of Physics and Electronic Information, Huanggang Normal University , Huanggang, China","institution_ids":["https://openalex.org/I10011244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101510848","display_name":"Chengxin Zhang","orcid":"https://orcid.org/0000-0001-7290-1324"},"institutions":[{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengxin Zhang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA"],"raw_orcid":"https://orcid.org/0000-0001-7290-1324","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I4210114445"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100354659","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-2739-1916"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Biological Chemistry, University of Michigan , Ann Arbor, MI, USA","Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, University of Michigan , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I4210114445"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100354659"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5943,"has_fulltext":false,"cited_by_count":102,"citation_normalized_percentile":{"value":0.83552259,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"35","issue":"21","first_page":"4459","last_page":"4461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9800000190734863,"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":0.9800000190734863,"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":0.006099999882280827,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.00419999985024333,"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":0.6789236664772034},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5562840104103088},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5451475977897644},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24826496839523315},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24622204899787903},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17465510964393616}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6789236664772034},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5562840104103088},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5451475977897644},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24826496839523315},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24622204899787903},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17465510964393616}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4459/30330744/btz282.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:31161212","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31161212","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:6821192","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821192","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4459/30330744/btz282.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":[],"awards":[{"id":"https://openalex.org/G155194203","display_name":null,"funder_award_id":"R01 GM116960","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1815782265","display_name":null,"funder_award_id":"R01GM083107","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2446008896","display_name":null,"funder_award_id":"31600592","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4408436485","display_name":null,"funder_award_id":"AI134678","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4509968318","display_name":null,"funder_award_id":"R01 AI134678","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5657833186","display_name":null,"funder_award_id":"GM116960","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7747661902","display_name":null,"funder_award_id":"DBI1564756","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8358395064","display_name":null,"funder_award_id":"GM083107","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1561493531","https://openalex.org/W2102245393","https://openalex.org/W2115540209","https://openalex.org/W2119916585","https://openalex.org/W2130350435","https://openalex.org/W2144698589","https://openalex.org/W2161151688","https://openalex.org/W2518705111","https://openalex.org/W2766848373","https://openalex.org/W2943097297","https://openalex.org/W6681254962"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"MOTIVATION:":[0],"Comparison":[1],"of":[2,13,17,33,101,108,120,129],"RNA":[3,14,20,50,62,130],"3D":[4,63],"structures":[5],"can":[6],"be":[7],"used":[8],"to":[9,48,124],"infer":[10],"functional":[11,36],"relationship":[12],"molecules.":[15],"Most":[16],"the":[18,31,39,43,68,105,109,114,125],"current":[19],"structure":[21,34,64,69,117,131],"alignment":[22,65,93,111],"programs":[23,44,90],"are":[24,122,141],"built":[25],"on":[26],"size-dependent":[27],"scales,":[28],"which":[29,66,121],"complicate":[30],"interpretation":[32],"and":[35,75,95,113,127],"relations.":[37],"Meanwhile,":[38],"low":[40],"speed":[41,126],"prevents":[42],"from":[45],"being":[46],"applied":[47],"large-scale":[49],"structural":[51],"database":[52],"search.":[53],"RESULTS:":[54],"We":[55],"developed":[56],"an":[57],"open-source":[58],"algorithm,":[59],"RNA-align,":[60],"for":[61],"has":[67],"similarity":[70],"scaled":[71],"by":[72],"a":[73],"size-independent":[74],"statistically":[76],"interpretable":[77],"scoring":[78],"metric.":[79],"Large-scale":[80],"benchmark":[81],"tests":[82],"show":[83],"that":[84],"RNA-align":[85,102],"significantly":[86],"outperforms":[87],"other":[88],"state-of-the-art":[89],"in":[91],"both":[92,119],"accuracy":[94,128],"running":[96],"speed.":[97],"The":[98],"major":[99],"advantage":[100],"lies":[103],"at":[104,143],"quick":[106],"convergence":[107],"heuristic":[110],"iterations":[112],"coarse-grained":[115],"secondary":[116],"assignment,":[118],"crucial":[123],"alignments.":[132],"AVAILABILITY":[133],"AND":[134],"IMPLEMENTATION:":[135],"https://zhanglab.ccmb.med.umich.edu/RNA-align/.":[136],"SUPPLEMENTARY":[137],"INFORMATION:":[138],"Supplementary":[139],"data":[140],"available":[142],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
