{"id":"https://openalex.org/W4401618248","doi":"https://doi.org/10.1007/s10462-024-10910-3","title":"Deep dive into RNA: a systematic literature review on RNA structure prediction using machine learning methods","display_name":"Deep dive into RNA: a systematic literature review on RNA structure prediction using machine learning methods","publication_year":2024,"publication_date":"2024-08-15","ids":{"openalex":"https://openalex.org/W4401618248","doi":"https://doi.org/10.1007/s10462-024-10910-3"},"language":"en","primary_location":{"id":"doi:10.1007/s10462-024-10910-3","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10462-024-10910-3","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10462-024-10910-3.pdf","source":{"id":"https://openalex.org/S122814990","display_name":"Artificial Intelligence Review","issn_l":"0269-2821","issn":["0269-2821","1573-7462"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Intelligence Review","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10462-024-10910-3.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106533812","display_name":"Micha\u0142 Budnik","orcid":null},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Micha\u0142 Budnik","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Pozna\u0144, Poland","TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Pozna\u0144, Poland","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102825222","display_name":"Jakub Wawrzyniak","orcid":"https://orcid.org/0000-0001-7664-9584"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jakub Wawrzyniak","raw_affiliation_strings":["TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106533813","display_name":"\u0141ukasz Grala","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"\u0141ukasz Grala","raw_affiliation_strings":["TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058649133","display_name":"Mi\u0142osz Kadzi\u0144ski","orcid":"https://orcid.org/0000-0003-1806-3715"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mi\u0142osz Kadzi\u0144ski","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Pozna\u0144, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Pozna\u0144, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051618054","display_name":"Natalia Sz\u00f3stak","orcid":"https://orcid.org/0000-0001-9933-0496"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Natalia Sz\u00f3stak","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704, Pozna\u0144, Poland","TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704, Pozna\u0144, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"TIDK Sp. z o.o., Ba\u0142tycka 6, 61-013, Pozna\u0144, Poland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5051618054"],"corresponding_institution_ids":["https://openalex.org/I4210152414"],"apc_list":{"value":2490,"currency":"EUR","value_usd":3090},"apc_paid":{"value":2490,"currency":"EUR","value_usd":3090},"fwci":2.2736,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.88470965,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"57","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994999766349792,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computer-science","display_name":"Computer science","score":0.6942551136016846},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5623501539230347},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4790938198566437},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.45895227789878845},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4573572874069214},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.42297476530075073},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10511323809623718}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6942551136016846},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5623501539230347},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4790938198566437},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.45895227789878845},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4573572874069214},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.42297476530075073},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10511323809623718},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s10462-024-10910-3","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10462-024-10910-3","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10462-024-10910-3.pdf","source":{"id":"https://openalex.org/S122814990","display_name":"Artificial Intelligence Review","issn_l":"0269-2821","issn":["0269-2821","1573-7462"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Intelligence Review","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s10462-024-10910-3","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10462-024-10910-3","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10462-024-10910-3.pdf","source":{"id":"https://openalex.org/S122814990","display_name":"Artificial Intelligence Review","issn_l":"0269-2821","issn":["0269-2821","1573-7462"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Intelligence Review","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4401618248.pdf","grobid_xml":"https://content.openalex.org/works/W4401618248.grobid-xml"},"referenced_works_count":132,"referenced_works":["https://openalex.org/W142718297","https://openalex.org/W1526127001","https://openalex.org/W1901129140","https://openalex.org/W1976961172","https://openalex.org/W1978967539","https://openalex.org/W1980410097","https://openalex.org/W1989454102","https://openalex.org/W1989949418","https://openalex.org/W1994958179","https://openalex.org/W1999608841","https://openalex.org/W2000191287","https://openalex.org/W2008652694","https://openalex.org/W2009215595","https://openalex.org/W2009265617","https://openalex.org/W2017838368","https://openalex.org/W2017965868","https://openalex.org/W2018838912","https://openalex.org/W2031352989","https://openalex.org/W2041882488","https://openalex.org/W2042881722","https://openalex.org/W2045777307","https://openalex.org/W2056742043","https://openalex.org/W2059099058","https://openalex.org/W2061103938","https://openalex.org/W2064675550","https://openalex.org/W2067258168","https://openalex.org/W2071271349","https://openalex.org/W2085115334","https://openalex.org/W2085235576","https://openalex.org/W2090041541","https://openalex.org/W2091735434","https://openalex.org/W2099374044","https://openalex.org/W2103894153","https://openalex.org/W2104846587","https://openalex.org/W2106478835","https://openalex.org/W2106595865","https://openalex.org/W2108688393","https://openalex.org/W2111976294","https://openalex.org/W2122377457","https://openalex.org/W2123241418","https://openalex.org/W2124374092","https://openalex.org/W2125952821","https://openalex.org/W2134510195","https://openalex.org/W2140505514","https://openalex.org/W2141152740","https://openalex.org/W2141157874","https://openalex.org/W2141411594","https://openalex.org/W2141607439","https://openalex.org/W2143726250","https://openalex.org/W2145339207","https://openalex.org/W2146721220","https://openalex.org/W2153140501","https://openalex.org/W2153268494","https://openalex.org/W2159117141","https://openalex.org/W2162224067","https://openalex.org/W2194775991","https://openalex.org/W2198606573","https://openalex.org/W2282821441","https://openalex.org/W2335029242","https://openalex.org/W2343186061","https://openalex.org/W2536860838","https://openalex.org/W2612690371","https://openalex.org/W2759571676","https://openalex.org/W2760363018","https://openalex.org/W2766448096","https://openalex.org/W2784570320","https://openalex.org/W2808896479","https://openalex.org/W2866340037","https://openalex.org/W2902320679","https://openalex.org/W2911293880","https://openalex.org/W2919479895","https://openalex.org/W2945901478","https://openalex.org/W2950954328","https://openalex.org/W2951298881","https://openalex.org/W2954092143","https://openalex.org/W2963707011","https://openalex.org/W2990045899","https://openalex.org/W2990528340","https://openalex.org/W2995183626","https://openalex.org/W2998238598","https://openalex.org/W3000918015","https://openalex.org/W3011821959","https://openalex.org/W3014154699","https://openalex.org/W3014847050","https://openalex.org/W3022554208","https://openalex.org/W3034567160","https://openalex.org/W3087202564","https://openalex.org/W3095979265","https://openalex.org/W3098223552","https://openalex.org/W3101505571","https://openalex.org/W3110563343","https://openalex.org/W3111119989","https://openalex.org/W3126773939","https://openalex.org/W3135161193","https://openalex.org/W3138796472","https://openalex.org/W3175812678","https://openalex.org/W3177828909","https://openalex.org/W3185104144","https://openalex.org/W3195438473","https://openalex.org/W3195820203","https://openalex.org/W3198907952","https://openalex.org/W3211639647","https://openalex.org/W3212533323","https://openalex.org/W3213615006","https://openalex.org/W4206427014","https://openalex.org/W4206601437","https://openalex.org/W4210378368","https://openalex.org/W4226341325","https://openalex.org/W4238219065","https://openalex.org/W4247001379","https://openalex.org/W4280513900","https://openalex.org/W4281294983","https://openalex.org/W4283523580","https://openalex.org/W4290672950","https://openalex.org/W4292707897","https://openalex.org/W4293194795","https://openalex.org/W4296164039","https://openalex.org/W4302362590","https://openalex.org/W4309788336","https://openalex.org/W4311276451","https://openalex.org/W4311376737","https://openalex.org/W4321210036","https://openalex.org/W4361223990","https://openalex.org/W4366082790","https://openalex.org/W4367322141","https://openalex.org/W4378349624","https://openalex.org/W4384405439","https://openalex.org/W4385068123","https://openalex.org/W6600018615","https://openalex.org/W6604545811","https://openalex.org/W6732880481","https://openalex.org/W6765940776"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W4321369474","https://openalex.org/W4360585206","https://openalex.org/W4285208911","https://openalex.org/W3046775127","https://openalex.org/W3082895349"],"abstract_inverted_index":{"Abstract":[0],"The":[1,17,138],"discovery":[2],"of":[3,11,35,43,54,100,121,129],"non-coding":[4],"RNAs":[5,23],"(ncRNAs)":[6],"has":[7],"expanded":[8],"our":[9],"comprehension":[10],"RNAs\u2019":[12],"inherent":[13],"nature":[14],"and":[15,28,135,159],"capabilities.":[16],"intricate":[18],"three-dimensional":[19],"structures":[20],"assumed":[21],"by":[22],"dictate":[24],"their":[25],"specific":[26],"functions":[27],"molecular":[29],"interactions.":[30,137],"However,":[31],"the":[32,52,98,113,127,152,161],"limited":[33],"number":[34],"mapped":[36],"structures,":[37,131],"partly":[38],"due":[39],"to":[40],"experimental":[41],"constraints":[42],"methods":[44,76,145],"such":[45],"as":[46,79],"nuclear":[47],"magnetic":[48],"resonance":[49],"(NMR),":[50],"highlights":[51,140],"importance":[53],"in":[55,63,66,86,112,143,156],"silico":[56],"prediction":[57],"solutions.":[58],"This":[59,93],"is":[60],"particularly":[61],"crucial":[62],"potential":[64],"applications":[65],"therapeutic":[67],"drug":[68],"discovery.":[69],"In":[70],"this":[71,157],"context,":[72],"machine":[73],"learning":[74,115],"(ML)":[75],"have":[77],"emerged":[78],"prominent":[80],"candidates,":[81],"having":[82],"previously":[83],"demonstrated":[84],"prowess":[85],"solving":[87],"complex":[88],"challenges":[89],"across":[90],"various":[91],"domains.":[92],"review":[94,139],"focuses":[95],"on":[96],"analyzing":[97],"development":[99],"ML-based":[101],"solutions":[102],"for":[103,147],"RNA":[104,130,148],"structure":[105,133,149],"prediction,":[106,150],"specifically":[107],"oriented":[108],"toward":[109],"recent":[110],"advancements":[111],"deep":[114],"(DL)":[116],"domain.":[117],"A":[118],"systematic":[119],"analysis":[120],"33":[122],"works":[123],"reveals":[124],"insights":[125],"into":[126],"representation":[128],"secondary":[132],"motifs,":[134],"tertiary":[136],"current":[141],"trends":[142],"ML":[144],"used":[146],"demonstrates":[151],"growing":[153],"research":[154],"involvement":[155],"field,":[158],"summarizes":[160],"most":[162],"valuable":[163],"findings.":[164]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8}],"updated_date":"2026-06-04T09:04:59.091469","created_date":"2025-10-10T00:00:00"}
