{"id":"https://openalex.org/W7160823493","doi":"https://doi.org/10.1093/bib/bbag226","title":"Accessibility in proteins and RNAs interactions prediction with machine learning: are we overlooking non-experts?","display_name":"Accessibility in proteins and RNAs interactions prediction with machine learning: are we overlooking non-experts?","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7160823493","doi":"https://doi.org/10.1093/bib/bbag226","pmid":"https://pubmed.ncbi.nlm.nih.gov/42108633"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag226","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag226","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag226","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5098753200","display_name":"Bruno Rafael Florentino","orcid":"https://orcid.org/0009-0006-0078-7634"},"institutions":[{"id":"https://openalex.org/I4210092357","display_name":"Institute of Mathematics and Computer Science","ror":"https://ror.org/00fy4at53","country_code":"MD","type":"facility","lineage":["https://openalex.org/I112090838","https://openalex.org/I4210092357"]},{"id":"https://openalex.org/I4210096256","display_name":"Office of Readiness and Response","ror":"https://ror.org/00sdb8f83","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210096256"]}],"countries":["MD","US"],"is_corresponding":false,"raw_author_name":"Bruno R Florentino","raw_affiliation_strings":["Global South Artificial Intelligence for Pandemic and Epidemic Preparedness & Response Network (AI4PEP)","Institute of Mathematical and Computer Sciences, University of S\u00e3o Paulo , Avenida Trabalhador S\u00e3o-Carlense 400, Centro, S\u00e3o Carlos, SP 13560-924 ,"],"raw_orcid":"https://orcid.org/0009-0006-0078-7634","affiliations":[{"raw_affiliation_string":"Global South Artificial Intelligence for Pandemic and Epidemic Preparedness & Response Network (AI4PEP)","institution_ids":["https://openalex.org/I4210096256"]},{"raw_affiliation_string":"Institute of Mathematical and Computer Sciences, University of S\u00e3o Paulo , Avenida Trabalhador S\u00e3o-Carlense 400, Centro, S\u00e3o Carlos, SP 13560-924 ,","institution_ids":["https://openalex.org/I4210092357"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076993536","display_name":"Robson Parmezan Bonidia","orcid":"https://orcid.org/0000-0003-4975-7867"},"institutions":[{"id":"https://openalex.org/I1283613182","display_name":"Universidade Tecnol\u00f3gica Federal do Paran\u00e1","ror":"https://ror.org/002v2kq79","country_code":"BR","type":"education","lineage":["https://openalex.org/I1283613182"]},{"id":"https://openalex.org/I4210092357","display_name":"Institute of Mathematics and Computer Science","ror":"https://ror.org/00fy4at53","country_code":"MD","type":"facility","lineage":["https://openalex.org/I112090838","https://openalex.org/I4210092357"]},{"id":"https://openalex.org/I4210096256","display_name":"Office of Readiness and Response","ror":"https://ror.org/00sdb8f83","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210096256"]}],"countries":["BR","MD","US"],"is_corresponding":true,"raw_author_name":"Robson P Bonidia","raw_affiliation_strings":["Department of Computer Science, Federal University of Technology-Paran\u00e1 (UTFPR) , Corn\u00e9lio Proc\u00f3pio 80230-901 ,","Global South Artificial Intelligence for Pandemic and Epidemic Preparedness & Response Network (AI4PEP)","Institute of Mathematical and Computer Sciences, University of S\u00e3o Paulo , Avenida Trabalhador S\u00e3o-Carlense 400, Centro, S\u00e3o Carlos, SP 13560-924 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Federal University of Technology-Paran\u00e1 (UTFPR) , Corn\u00e9lio Proc\u00f3pio 80230-901 ,","institution_ids":["https://openalex.org/I1283613182"]},{"raw_affiliation_string":"Global South Artificial Intelligence for Pandemic and Epidemic Preparedness & Response Network (AI4PEP)","institution_ids":["https://openalex.org/I4210096256"]},{"raw_affiliation_string":"Institute of Mathematical and Computer Sciences, University of S\u00e3o Paulo , Avenida Trabalhador S\u00e3o-Carlense 400, Centro, S\u00e3o Carlos, SP 13560-924 ,","institution_ids":["https://openalex.org/I4210092357"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5135839443","display_name":"Andr\u00e9 C P L F de Carvalho","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092357","display_name":"Institute of Mathematics and Computer Science","ror":"https://ror.org/00fy4at53","country_code":"MD","type":"facility","lineage":["https://openalex.org/I112090838","https://openalex.org/I4210092357"]},{"id":"https://openalex.org/I4210096256","display_name":"Office of Readiness and Response","ror":"https://ror.org/00sdb8f83","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210096256"]}],"countries":["MD","US"],"is_corresponding":true,"raw_author_name":"Andr\u00e9 C P L F de Carvalho","raw_affiliation_strings":["Global South Artificial Intelligence for Pandemic and Epidemic Preparedness & Response Network (AI4PEP)","Institute of Mathematical and Computer Sciences, University of S\u00e3o Paulo , Avenida Trabalhador S\u00e3o-Carlense 400, Centro, S\u00e3o Carlos, SP 13560-924 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global South Artificial Intelligence for Pandemic and Epidemic Preparedness & Response Network (AI4PEP)","institution_ids":["https://openalex.org/I4210096256"]},{"raw_affiliation_string":"Institute of Mathematical and Computer Sciences, University of S\u00e3o Paulo , Avenida Trabalhador S\u00e3o-Carlense 400, Centro, S\u00e3o Carlos, SP 13560-924 ,","institution_ids":["https://openalex.org/I4210092357"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076993536","https://openalex.org/A5135839443"],"corresponding_institution_ids":["https://openalex.org/I1283613182","https://openalex.org/I4210092357","https://openalex.org/I4210096256"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.61706895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.29319998621940613,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.29319998621940613,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.18209999799728394,"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":0.10930000245571136,"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/identification","display_name":"Identification (biology)","score":0.6470999717712402},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.6252999901771545},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.46790000796318054},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4675000011920929},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4512999951839447},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.3781999945640564}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7925999760627747},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6470999717712402},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.6252999901771545},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47699999809265137},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.46790000796318054},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4675000011920929},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4641999900341034},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4512999951839447},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4300000071525574},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3781999945640564},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.35830000042915344},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.35199999809265137},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.33480000495910645},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.32280001044273376},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.31869998574256897},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.30469998717308044},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.2906000018119812}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag226","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag226","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42108633","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42108633","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13158124","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13158124/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag226","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag226","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G434531211","display_name":null,"funder_award_id":"88887.951910/2024-00","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"},{"id":"https://openalex.org/G5132246973","display_name":"IARA - Artificial Intelligence in the Remaking of Urban Environments","funder_award_id":"20/09835-1","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":77,"referenced_works":["https://openalex.org/W30210889","https://openalex.org/W2101086441","https://openalex.org/W2106956101","https://openalex.org/W2123500593","https://openalex.org/W2150882562","https://openalex.org/W2161159766","https://openalex.org/W2233915997","https://openalex.org/W2572080171","https://openalex.org/W2615136515","https://openalex.org/W2749836266","https://openalex.org/W2771169143","https://openalex.org/W2784570320","https://openalex.org/W2786937803","https://openalex.org/W2908390949","https://openalex.org/W2950389803","https://openalex.org/W2950742983","https://openalex.org/W2957436444","https://openalex.org/W2998220730","https://openalex.org/W3035353528","https://openalex.org/W3037097018","https://openalex.org/W3038935757","https://openalex.org/W3045012301","https://openalex.org/W3080365360","https://openalex.org/W3081019734","https://openalex.org/W3087769169","https://openalex.org/W3092273386","https://openalex.org/W3121391924","https://openalex.org/W3130271948","https://openalex.org/W3185942550","https://openalex.org/W3194280519","https://openalex.org/W3209369100","https://openalex.org/W3215058137","https://openalex.org/W4200353319","https://openalex.org/W4205177317","https://openalex.org/W4213041764","https://openalex.org/W4220660070","https://openalex.org/W4226213429","https://openalex.org/W4282927263","https://openalex.org/W4283584023","https://openalex.org/W4292075180","https://openalex.org/W4292089263","https://openalex.org/W4294636450","https://openalex.org/W4295107433","https://openalex.org/W4306938197","https://openalex.org/W4309419452","https://openalex.org/W4317703013","https://openalex.org/W4321851522","https://openalex.org/W4323348775","https://openalex.org/W4324311365","https://openalex.org/W4327718177","https://openalex.org/W4375955768","https://openalex.org/W4376649056","https://openalex.org/W4380881660","https://openalex.org/W4385707729","https://openalex.org/W4386209142","https://openalex.org/W4387966090","https://openalex.org/W4389166162","https://openalex.org/W4389816980","https://openalex.org/W4392694717","https://openalex.org/W4392714934","https://openalex.org/W4394014430","https://openalex.org/W4394906309","https://openalex.org/W4398202116","https://openalex.org/W4399167256","https://openalex.org/W4400984795","https://openalex.org/W4401794303","https://openalex.org/W4404511387","https://openalex.org/W4405516947","https://openalex.org/W4406172247","https://openalex.org/W4408522311","https://openalex.org/W4409064035","https://openalex.org/W4411962794","https://openalex.org/W4412877878","https://openalex.org/W4413412856","https://openalex.org/W4413775728","https://openalex.org/W4415532145","https://openalex.org/W7117146061"],"related_works":[],"abstract_inverted_index":{"The":[0],"increasing":[1],"growth":[2],"in":[3,19,53,56,79,98,134,155,185],"the":[4,60,73,91,140,164,172,183],"volume":[5],"of":[6,62,76,145,167,174,202,225],"biomolecular":[7],"data":[8],"has":[9,48,87],"introduced":[10],"significant":[11],"challenges":[12],"for":[13,110,123,149],"extracting":[14],"meaningful":[15],"molecular-level":[16],"insights,":[17],"particularly":[18],"predicting":[20],"interactions":[21,32],"between":[22],"biological":[23,37,135],"sequences":[24],"such":[25],"as":[26,65],"DNA,":[27],"RNA,":[28],"and":[29,42,113,143,162],"proteins.":[30],"These":[31],"are":[33,152],"fundamental":[34],"to":[35,83,180,198,205,220],"complex":[36],"processes,":[38],"including":[39],"gene":[40],"regulation":[41],"immune":[43],"response.":[44],"Artificial":[45],"Intelligence":[46],"(AI)":[47],"played":[49],"a":[50,115],"major":[51],"role":[52],"advancing":[54],"discoveries":[55],"this":[57,80,127,129],"field,":[58],"enabling":[59,178],"identification":[61],"novel":[63],"interactions,":[64],"demonstrated":[66],"by":[67],"various":[68],"predictive":[69],"modeling":[70],"studies.":[71],"Despite":[72],"growing":[74],"number":[75,117],"scientific":[77],"publications":[78],"domain,":[81],"accessibility":[82,142],"practical":[84],"computational":[85,158,218],"tools":[86,203],"not":[88,153],"progressed":[89],"at":[90],"same":[92],"pace.":[93],"Existing":[94],"studies":[95,133],"differ":[96],"substantially":[97],"availability:":[99],"some":[100],"provide":[101],"only":[102,114],"methodological":[103],"descriptions,":[104],"others":[105],"release":[106],"source":[107],"code":[108],"exclusively":[109],"experimental":[111],"reproducibility,":[112],"limited":[116],"deliver":[118],"fully":[119,221],"automated":[120],"solutions":[121],"ready":[122],"broad":[124],"use.":[125],"Given":[126],"context,":[128],"paper":[130],"investigates":[131],"state-of-the-art":[132],"sequence":[136],"interaction":[137],"prediction,":[138],"emphasizing":[139],"public":[141],"usability":[144],"available":[146],"tools,":[147,169],"especially":[148],"researchers":[150],"who":[151],"experts":[154],"AI":[156],"or":[157],"methods.":[159],"We":[160],"compile":[161],"discuss":[163],"input":[165],"requirements":[166],"current":[168],"along":[170],"with":[171,212],"types":[173],"outputs":[175],"they":[176],"generate,":[177],"users":[179],"better":[181],"understand":[182],"scenarios":[184],"which":[186],"each":[187],"solution":[188],"can":[189],"be":[190],"effectively":[191],"applied.":[192],"Furthermore,":[193],"we":[194],"analyze":[195],"accessibility-related":[196],"aspects":[197],"support":[199],"informed":[200],"selection":[201],"according":[204],"user":[206],"expertise,":[207],"ranging":[208],"from":[209],"web-based":[210],"servers":[211],"pretrained":[213],"models":[214,228],"that":[215],"require":[216],"minimal":[217],"skills":[219],"end-to-end":[222],"frameworks":[223],"capable":[224],"training":[226],"new":[227],"on":[229],"user-defined":[230],"datasets,":[231],"though":[232],"often":[233],"lacking":[234],"user-friendly":[235],"interfaces.":[236]},"counts_by_year":[],"updated_date":"2026-06-25T08:15:23.626066","created_date":"2026-05-12T00:00:00"}
