{"id":"https://openalex.org/W2949401548","doi":"https://doi.org/10.3389/fgene.2017.00147","title":"An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences","display_name":"An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences","publication_year":2017,"publication_date":"2017-10-10","ids":{"openalex":"https://openalex.org/W2949401548","doi":"https://doi.org/10.3389/fgene.2017.00147","mag":"2949401548","pmid":"https://pubmed.ncbi.nlm.nih.gov/29067038","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5641303"},"language":"en","primary_location":{"id":"doi:10.3389/fgene.2017.00147","doi":"https://doi.org/10.3389/fgene.2017.00147","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fgene.2017.00147","pdf_url":"https://www.frontiersin.org/articles/10.3389/fgene.2017.00147/pdf","source":{"id":"https://openalex.org/S2597340651","display_name":"Frontiers in Genetics","issn_l":"1664-8021","issn":["1664-8021"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Genetics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fgene.2017.00147/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058440863","display_name":"Josef P\u00e1nek","orcid":"https://orcid.org/0000-0002-3388-3570","observed_orcids":["https://orcid.org/0000-0002-3388-3570"]},"institutions":[{"id":"https://openalex.org/I202391551","display_name":"Czech Academy of Sciences","ror":"https://ror.org/053avzc18","country_code":"CZ","type":"government","lineage":["https://openalex.org/I202391551"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Josef P\u00e1nek","raw_affiliation_strings":["Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, Prague, Czechia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, Prague, Czechia","institution_ids":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070226118","display_name":"Martin Modr\u00e1k","orcid":"https://orcid.org/0000-0002-8886-7797","observed_orcids":["https://orcid.org/0000-0002-8886-7797"]},"institutions":[{"id":"https://openalex.org/I202391551","display_name":"Czech Academy of Sciences","ror":"https://ror.org/053avzc18","country_code":"CZ","type":"government","lineage":["https://openalex.org/I202391551"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Martin Modr\u00e1k","raw_affiliation_strings":["Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, Prague, Czechia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, Prague, Czechia","institution_ids":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022032071","display_name":"Marek Schwarz","orcid":"https://orcid.org/0000-0002-3300-6260","observed_orcids":["https://orcid.org/0000-0002-3300-6260"]},"institutions":[{"id":"https://openalex.org/I202391551","display_name":"Czech Academy of Sciences","ror":"https://ror.org/053avzc18","country_code":"CZ","type":"government","lineage":["https://openalex.org/I202391551"]},{"id":"https://openalex.org/I4210122847","display_name":"Czech Academy of Sciences, Institute of Microbiology","ror":"https://ror.org/02p1jz666","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Marek Schwarz","raw_affiliation_strings":["Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, Prague, Czechia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, Prague, Czechia","institution_ids":["https://openalex.org/I202391551","https://openalex.org/I4210122847"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058440863"],"corresponding_institution_ids":["https://openalex.org/I202391551","https://openalex.org/I4210122847"],"apc_list":{"value":3150,"currency":"CHF","value_usd":3801},"apc_paid":{"value":3150,"currency":"CHF","value_usd":3801},"fwci":0.2921,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.49780844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"8","issue":null,"first_page":"147","last_page":"147"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9970999956130981,"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":0.9970999956130981,"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":0.00039999998989515007,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0003000000142492354,"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-secondary-structure-prediction","display_name":"RNA secondary structure prediction","score":0.9959999918937683},{"id":"https://openalex.org/keywords/template-based-modeling","display_name":"template-based modeling","score":0.9139999747276306},{"id":"https://openalex.org/keywords/evolutionary-conservation","display_name":"evolutionary conservation","score":0.7680000066757202},{"id":"https://openalex.org/keywords/de-novo-structure-prediction","display_name":"de novo structure prediction","score":0.875},{"id":"https://openalex.org/keywords/prediction-reliability","display_name":"forecast reliability","score":0.5820000171661377}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7347099184989929},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.674490749835968},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6326144933700562},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5858269929885864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5341777801513672},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5264254808425903},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4740076959133148},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2706509828567505},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13953885436058044},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11698734760284424},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.3389/fgene.2017.00147","doi":"https://doi.org/10.3389/fgene.2017.00147","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fgene.2017.00147","pdf_url":"https://www.frontiersin.org/articles/10.3389/fgene.2017.00147/pdf","source":{"id":"https://openalex.org/S2597340651","display_name":"Frontiers in Genetics","issn_l":"1664-8021","issn":["1664-8021"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Genetics","raw_type":"journal-article"},{"id":"doi:10.1101/171108","doi":"https://doi.org/10.1101/171108","is_oa":true,"landing_page_url":"https://doi.org/10.1101/171108","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2017/08/01/171108.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:29067038","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29067038","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,"listed_in":[],"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":"Frontiers in genetics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5641303","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5641303/","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Front Genet","raw_type":"Text"},{"id":"pmh:oai:asep.lib.cas.cz:CavUnEpca/0480493","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/11104/0276346","pdf_url":null,"source":{"id":"https://openalex.org/S7407055266","display_name":"ASEP","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:e109a2da5fed4f078015909a202730eb","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/e109a2da5fed4f078015909a202730eb","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,"listed_in":[],"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":"Frontiers in Genetics, Vol 8 (2017)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fgene.2017.00147","doi":"https://doi.org/10.3389/fgene.2017.00147","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fgene.2017.00147","pdf_url":"https://www.frontiersin.org/articles/10.3389/fgene.2017.00147/pdf","source":{"id":"https://openalex.org/S2597340651","display_name":"Frontiers in Genetics","issn_l":"1664-8021","issn":["1664-8021"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Genetics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2061811189","display_name":null,"funder_award_id":"LM2015047","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G5384873034","display_name":"Novel methods for computational prediction and visualization of secondary structures of ribosomal ribonucleic acids - an integrated solution","funder_award_id":"GA15-00885S","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G6170670103","display_name":"Czech National Infrastructure for Biological Data","funder_award_id":"LM2015047","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949401548.pdf","grobid_xml":"https://content.openalex.org/works/W2949401548.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1585306636","https://openalex.org/W1930039709","https://openalex.org/W1976021976","https://openalex.org/W2009215595","https://openalex.org/W2028102516","https://openalex.org/W2034393805","https://openalex.org/W2038598202","https://openalex.org/W2046335009","https://openalex.org/W2086561953","https://openalex.org/W2098553089","https://openalex.org/W2101535367","https://openalex.org/W2104702173","https://openalex.org/W2106612397","https://openalex.org/W2106882534","https://openalex.org/W2108895594","https://openalex.org/W2131054067","https://openalex.org/W2141152740","https://openalex.org/W2143407915","https://openalex.org/W2159548583","https://openalex.org/W2166745309","https://openalex.org/W2492384598","https://openalex.org/W2751326462","https://openalex.org/W2752932982","https://openalex.org/W2970966356"],"related_works":["https://openalex.org/W2001187219","https://openalex.org/W800800553","https://openalex.org/W2523429666","https://openalex.org/W2183625742","https://openalex.org/W3209002005","https://openalex.org/W2893598653","https://openalex.org/W2129657054","https://openalex.org/W1824702766","https://openalex.org/W2477581633","https://openalex.org/W1971346501"],"abstract_inverted_index":{"While":[0],"understanding":[1],"the":[2,21,79,86,96,108,124],"structure":[3,29,56,58,81,88,94,110],"of":[4,53,59,123,128,144,161,164],"RNA":[5,14,28,55,74,166],"molecules":[6,61],"is":[7,17,82,111,115,137,150],"vital":[8],"for":[9,95,156],"deciphering":[10],"their":[11],"functions,":[12],"determining":[13],"structures":[15,163],"experimentally":[16,118],"exceptionally":[18],"hard.":[19],"At":[20],"same":[22],"time,":[23],"extant":[24],"approaches":[25],"to":[26,43],"computational":[27],"prediction":[30,52,130,134],"have":[31],"limited":[32],"applicability":[33],"and":[34,69,89,132,152,154],"reliability.":[35],"In":[36],"this":[37],"paper":[38],"we":[39],"provide":[40],"a":[41,45,63],"method":[42,66,104,114,125,149],"solve":[44],"simpler":[46],"yet":[47],"still":[48],"biologically":[49],"relevant":[50],"problem:":[51],"secondary":[54,162],"using":[57,117,141],"different":[60],"as":[62],"template.":[64],"Our":[65],"identifies":[67],"conserved":[68,77],"unconserved":[70,97],"subsequences":[71,98],"within":[72],"an":[73],"molecule.":[75],"For":[76],"subsequences,":[78],"template":[80],"directly":[83],"transferred":[84],"into":[85],"generated":[87,109],"combined":[90],"with":[91,99],"de-novo":[92],"predicted":[93],"low":[100],"evolutionary":[101],"conservation.":[102],"The":[103,113,121,147],"also":[105],"determines,":[106],"when":[107],"unreliable.":[112],"validated":[116],"identified":[119],"structures.":[120],"accuracy":[122],"exceeds":[126],"that":[127],"classical":[129],"algorithms":[131],"constrained":[133],"methods.":[135],"This":[136],"demonstrated":[138],"by":[139],"comparison":[140],"large":[142],"number":[143],"heterogeneous":[145],"RNAs.":[146],"presented":[148],"fast":[151],"robust,":[153],"useful":[155],"various":[157],"applications":[158],"requiring":[159],"knowledge":[160],"individual":[165],"sequences.":[167]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2019-06-27T00:00:00"}
