{"id":"https://openalex.org/W2176670566","doi":"https://doi.org/10.3390/e17117827","title":"Theoretical Search for RNA Folding Nuclei","display_name":"Theoretical Search for RNA Folding Nuclei","publication_year":2015,"publication_date":"2015-11-23","ids":{"openalex":"https://openalex.org/W2176670566","doi":"https://doi.org/10.3390/e17117827","mag":"2176670566"},"language":"en","primary_location":{"id":"doi:10.3390/e17117827","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e17117827","pdf_url":"https://www.mdpi.com/1099-4300/17/11/7827/pdf?version=1448284881","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/17/11/7827/pdf?version=1448284881","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028096134","display_name":"Leonid Pereyaslavets","orcid":"https://orcid.org/0000-0001-5410-2318"},"institutions":[{"id":"https://openalex.org/I4210137602","display_name":"Institute of Protein Research","ror":"https://ror.org/0489f0s93","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210137602"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Leonid Pereyaslavets","raw_affiliation_strings":["Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia"],"affiliations":[{"raw_affiliation_string":"Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia","institution_ids":["https://openalex.org/I4210137602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023828983","display_name":"Oxana V. Galzitskaya","orcid":"https://orcid.org/0000-0002-3962-1520"},"institutions":[{"id":"https://openalex.org/I4210137602","display_name":"Institute of Protein Research","ror":"https://ror.org/0489f0s93","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210137602"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Oxana Galzitskaya","raw_affiliation_strings":["Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia"],"affiliations":[{"raw_affiliation_string":"Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia","institution_ids":["https://openalex.org/I4210137602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5023828983"],"corresponding_institution_ids":["https://openalex.org/I4210137602"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.06087203,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"17","issue":"11","first_page":"7827","last_page":"7847"},"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":0.9987999796867371,"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":0.9975000023841858,"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":0.8269798159599304},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.6547365188598633},{"id":"https://openalex.org/keywords/tetrahymena","display_name":"Tetrahymena","score":0.6319370865821838},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5415592193603516},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5343438982963562},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.5174918174743652},{"id":"https://openalex.org/keywords/ribozyme","display_name":"Ribozyme","score":0.4302443861961365},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.41996410489082336},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37725743651390076},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.36918091773986816},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3685852289199829},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3652890920639038},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.28840917348861694},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24348220229148865},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1423991620540619}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.8269798159599304},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.6547365188598633},{"id":"https://openalex.org/C2777166614","wikidata":"https://www.wikidata.org/wiki/Q1198419","display_name":"Tetrahymena","level":2,"score":0.6319370865821838},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5415592193603516},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5343438982963562},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.5174918174743652},{"id":"https://openalex.org/C76346623","wikidata":"https://www.wikidata.org/wiki/Q205858","display_name":"Ribozyme","level":4,"score":0.4302443861961365},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.41996410489082336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37725743651390076},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.36918091773986816},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3685852289199829},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3652890920639038},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.28840917348861694},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24348220229148865},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1423991620540619},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/e17117827","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e17117827","pdf_url":"https://www.mdpi.com/1099-4300/17/11/7827/pdf?version=1448284881","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:39431410b54246fea97ce8a35082d3a3","is_oa":true,"landing_page_url":"https://doaj.org/article/39431410b54246fea97ce8a35082d3a3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy, Vol 17, Iss 11, Pp 7827-7847 (2015)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/17/11/7827/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/e17117827","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Entropy","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e17117827","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e17117827","pdf_url":"https://www.mdpi.com/1099-4300/17/11/7827/pdf?version=1448284881","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3553171911","display_name":null,"funder_award_id":"14-14-00536","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2176670566.pdf","grobid_xml":"https://content.openalex.org/works/W2176670566.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W175066646","https://openalex.org/W598131573","https://openalex.org/W1516459493","https://openalex.org/W1530704185","https://openalex.org/W1550166367","https://openalex.org/W1569560802","https://openalex.org/W1963688013","https://openalex.org/W1966307609","https://openalex.org/W1967689204","https://openalex.org/W1969243198","https://openalex.org/W1970680503","https://openalex.org/W1977940795","https://openalex.org/W1981292959","https://openalex.org/W1984675364","https://openalex.org/W1990351127","https://openalex.org/W1990644981","https://openalex.org/W1991999468","https://openalex.org/W2000123367","https://openalex.org/W2007577495","https://openalex.org/W2008440654","https://openalex.org/W2009818318","https://openalex.org/W2021057901","https://openalex.org/W2024196584","https://openalex.org/W2025763720","https://openalex.org/W2029871341","https://openalex.org/W2039920077","https://openalex.org/W2048683276","https://openalex.org/W2059820046","https://openalex.org/W2061712144","https://openalex.org/W2061837730","https://openalex.org/W2071889630","https://openalex.org/W2074882547","https://openalex.org/W2076430296","https://openalex.org/W2078960884","https://openalex.org/W2082271368","https://openalex.org/W2083969154","https://openalex.org/W2094517427","https://openalex.org/W2105393940","https://openalex.org/W2110790388","https://openalex.org/W2112032866","https://openalex.org/W2119461177","https://openalex.org/W2119881887","https://openalex.org/W2120974004","https://openalex.org/W2122602899","https://openalex.org/W2122951823","https://openalex.org/W2123241418","https://openalex.org/W2127270490","https://openalex.org/W2134036931","https://openalex.org/W2134489577","https://openalex.org/W2142421949","https://openalex.org/W2142852652","https://openalex.org/W2148265110","https://openalex.org/W2154845100","https://openalex.org/W2157467256","https://openalex.org/W2165222310","https://openalex.org/W2169186845","https://openalex.org/W2169751581","https://openalex.org/W2409572347","https://openalex.org/W2429609256","https://openalex.org/W2465621576","https://openalex.org/W3103544692","https://openalex.org/W3106148129","https://openalex.org/W6670349568"],"related_works":["https://openalex.org/W2391352090","https://openalex.org/W2016336073","https://openalex.org/W2160523873","https://openalex.org/W18387404","https://openalex.org/W2028080628","https://openalex.org/W2034372974","https://openalex.org/W2037720860","https://openalex.org/W4317529025","https://openalex.org/W2132966204","https://openalex.org/W2002128365"],"abstract_inverted_index":{"The":[0,51,88],"functions":[1],"of":[2,25,40,45,57,81,107,136,145,148],"RNA":[3,19,26,46,49,68,142,165],"molecules":[4,47],"are":[5,114],"defined":[6],"by":[7,15],"their":[8],"spatial":[9],"structure,":[10],"whose":[11],"folding":[12,27,43,59,161],"is":[13,151],"regulated":[14],"numerous":[16],"factors":[17],"making":[18],"very":[20],"similar":[21],"to":[22,32,65,102,117,129,156],"proteins.":[23],"Prediction":[24],"nuclei":[28,60],"gives":[29],"the":[30,38,41,76,82,96,103,105,108,115,121,140,146,160],"possibility":[31],"take":[33],"a":[34,131],"fresh":[35],"look":[36],"at":[37],"problems":[39],"multiple":[42],"pathways":[44],"and":[48,75,110,168],"stability.":[50],"algorithm":[52],"previously":[53],"developed":[54],"for":[55,91,133,163],"prediction":[56,132],"protein":[58],"has":[61],"been":[62],"successfully":[63],"applied":[64],"~150":[66],"various":[67],"structures:":[69],"hairpins,":[70],"tRNAs,":[71],"structures":[72,93],"with":[73,95],"pseudoknots,":[74],"large":[77,137],"structured":[78,138],"P4-P6":[79,141],"domain":[80],"Tetrahymena":[83],"group":[84],"I":[85],"intron":[86],"RNA.":[87],"calculated":[89],"\u03a6-values":[90],"tRNA":[92,122],"agree":[94],"experimental":[97],"data":[98],"obtained":[99],"earlier.":[100],"According":[101],"experiment":[104],"nucleotides":[106],"D":[109],"T":[111],"hairpin":[112],"loops":[113],"last":[116],"be":[118],"involved":[119],"in":[120],"tertiary":[123],"structure.":[124],"Such":[125],"agreement":[126],"allowed":[127],"us":[128,155],"do":[130],"an":[134],"example":[135],"RNA,":[139],"domain.":[143],"One":[144],"advantages":[147],"our":[149],"method":[150],"that":[152],"it":[153],"allows":[154],"make":[157],"predictions":[158],"about":[159],"nucleus":[162],"nontrivial":[164],"motifs:":[166],"pseudoknots":[167],"tRNA.":[169]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}