{"id":"https://openalex.org/W2122558818","doi":"https://doi.org/10.1093/bioinformatics/bts301","title":"Efficient RNA pairwise structure comparison by SETTER method","display_name":"Efficient RNA pairwise structure comparison by SETTER method","publication_year":2012,"publication_date":"2012-05-18","ids":{"openalex":"https://openalex.org/W2122558818","doi":"https://doi.org/10.1093/bioinformatics/bts301","mag":"2122558818","pmid":"https://pubmed.ncbi.nlm.nih.gov/22611129"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts301","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/bts301","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/14/1858/48873939/bioinformatics_28_14_1858.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/28/14/1858/48873939/bioinformatics_28_14_1858.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049617942","display_name":"David Hoksza","orcid":"https://orcid.org/0000-0003-4679-0557"},"institutions":[{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]},{"id":"https://openalex.org/I9073902","display_name":"University of Chemistry and Technology, Prague","ror":"https://ror.org/05ggn0a85","country_code":"CZ","type":"education","lineage":["https://openalex.org/I9073902"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"David Hoksza","raw_affiliation_strings":["1 SIRET Research Group, Department of Software Engineering, FMP, Charles University in Prague, 11800 Czech Republic and 2Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, 16628 Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 SIRET Research Group, Department of Software Engineering, FMP, Charles University in Prague, 11800 Czech Republic and 2Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, 16628 Czech Republic","institution_ids":["https://openalex.org/I9073902","https://openalex.org/I21250087"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082393460","display_name":"Daniel Svozil","orcid":"https://orcid.org/0000-0003-2577-5163"},"institutions":[{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]},{"id":"https://openalex.org/I9073902","display_name":"University of Chemistry and Technology, Prague","ror":"https://ror.org/05ggn0a85","country_code":"CZ","type":"education","lineage":["https://openalex.org/I9073902"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Daniel Svozil","raw_affiliation_strings":["1 SIRET Research Group, Department of Software Engineering, FMP, Charles University in Prague, 11800 Czech Republic and 2Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, 16628 Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 SIRET Research Group, Department of Software Engineering, FMP, Charles University in Prague, 11800 Czech Republic and 2Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, 16628 Czech Republic","institution_ids":["https://openalex.org/I9073902","https://openalex.org/I21250087"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4782,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.81685971,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"14","first_page":"1858","last_page":"1864"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9628999829292297,"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":0.9628999829292297,"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":0.010999999940395355,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.003800000064074993,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/setter","display_name":"Setter","score":0.9681267738342285},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.8033100366592407},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7562263011932373},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6272651553153992},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.5489266514778137},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5056593418121338},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4619247317314148},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4202898442745209},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37792736291885376},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3333396017551422},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.333034485578537},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.21077647805213928},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13415667414665222},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.09386575222015381}],"concepts":[{"id":"https://openalex.org/C2780667275","wikidata":"https://www.wikidata.org/wiki/Q39640","display_name":"Setter","level":2,"score":0.9681267738342285},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.8033100366592407},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7562263011932373},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6272651553153992},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.5489266514778137},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5056593418121338},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4619247317314148},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4202898442745209},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37792736291885376},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3333396017551422},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.333034485578537},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.21077647805213928},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13415667414665222},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.09386575222015381},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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":"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":"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D017423","descriptor_name":"Sequence Analysis, RNA","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts301","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/bts301","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/14/1858/48873939/bioinformatics_28_14_1858.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:22611129","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22611129","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:zenodo.org:890287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts301","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts301","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/bts301","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/14/1858/48873939/bioinformatics_28_14_1858.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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2122558818.pdf","grobid_xml":"https://content.openalex.org/works/W2122558818.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1559074274","https://openalex.org/W1983029427","https://openalex.org/W1988884185","https://openalex.org/W2008763023","https://openalex.org/W2027042879","https://openalex.org/W2049811404","https://openalex.org/W2052841473","https://openalex.org/W2061770640","https://openalex.org/W2072737163","https://openalex.org/W2074718022","https://openalex.org/W2081766794","https://openalex.org/W2082589966","https://openalex.org/W2100981947","https://openalex.org/W2101524130","https://openalex.org/W2106595865","https://openalex.org/W2108927984","https://openalex.org/W2119274978","https://openalex.org/W2119896557","https://openalex.org/W2119916585","https://openalex.org/W2120418017","https://openalex.org/W2124050695","https://openalex.org/W2130350435","https://openalex.org/W2133296358","https://openalex.org/W2134874046","https://openalex.org/W2136567909","https://openalex.org/W2144366714","https://openalex.org/W2158698691","https://openalex.org/W2167040380","https://openalex.org/W2464156486","https://openalex.org/W2582743722","https://openalex.org/W2611102240","https://openalex.org/W4237468509","https://openalex.org/W6719535422"],"related_works":["https://openalex.org/W2743258233","https://openalex.org/W3183633970","https://openalex.org/W2122558818","https://openalex.org/W2154685897","https://openalex.org/W2104016334","https://openalex.org/W2090617952","https://openalex.org/W2259085479","https://openalex.org/W3032097558","https://openalex.org/W1975453400","https://openalex.org/W4294795463"],"abstract_inverted_index":{"MOTIVATION:":[0],"Understanding":[1],"the":[2,40,43,50,55,107,136,173],"architecture":[3],"and":[4,13,59,123,156,165,167],"function":[5],"of":[6,22,31,42,45,57,106,116,126,139,175],"RNA":[7,84,177],"molecules":[8],"requires":[9],"methods":[10,61],"for":[11,54,62,69,82,135,151],"comparing":[12],"analyzing":[14,63],"their":[15,64],"3D":[16,104,152],"structures.":[17,178],"Although":[18],"a":[19,28,79,98,120],"structural":[20,85,137],"alignment":[21],"short":[23],"RNAs":[24,47],"is":[25,94,162,188],"achievable":[26],"in":[27,49,73],"reasonable":[29],"amount":[30],"time,":[32],"large":[33,46],"structures":[34,140],"represent":[35],"much":[36],"bigger":[37],"challenge.":[38],"However,":[39],"growth":[41],"number":[44],"deposited":[48],"PDB":[51],"database":[52],"calls":[53],"development":[56],"fast":[58,166],"accurate":[60,164],"structures,":[65,117],"as":[66,68,148,150,183,185],"well":[67,149,184],"rapid":[70],"similarity":[71,105,154],"searches":[72,155],"databases.":[74],"RESULTS:":[75],"In":[76],"this":[77],"article":[78],"novel":[80],"algorithm":[81,160],"an":[83,124],"comparison":[86,100],"SETTER":[87,96,118,130,181],"(SEcondary":[88],"sTructure-based":[89],"TERtiary":[90],"Structure":[91],"Similarity":[92],"Algorithm)":[93],"introduced.":[95],"uses":[97],"pairwise":[99],"method":[101],"based":[102],"on":[103,172],"so-called":[108],"generalized":[109],"secondary":[110],"structure":[111,153],"units.":[112],"For":[113],"each":[114],"pair":[115],"produces":[119],"distance":[121],"score":[122],"indication":[125],"its":[127],"statistical":[128],"significance.":[129],"can":[131],"be":[132,146],"used":[133],"both":[134,163],"alignments":[138],"that":[141],"are":[142],"already":[143],"known":[144],"to":[145],"homologous,":[147],"functional":[157],"annotation.":[158],"The":[159,180],"presented":[161],"does":[168],"not":[169],"impose":[170],"limits":[171],"size":[174],"aligned":[176],"AVAILABILITY:":[179],"program,":[182],"all":[186],"datasets,":[187],"freely":[189],"available":[190],"from":[191],"http://siret.cz/hoksza/projects/setter/.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
