{"id":"https://openalex.org/W4389049678","doi":"https://doi.org/10.1186/s12859-023-05577-6","title":"AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders","display_name":"AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders","publication_year":2023,"publication_date":"2023-11-27","ids":{"openalex":"https://openalex.org/W4389049678","doi":"https://doi.org/10.1186/s12859-023-05577-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/38012571"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05577-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05577-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05577-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05577-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068700705","display_name":"Incheol Shin","orcid":"https://orcid.org/0000-0003-3172-2594"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Incheol Shin","raw_affiliation_strings":["Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104192468","display_name":"Keumseok Kang","orcid":null},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Keumseok Kang","raw_affiliation_strings":["Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002384612","display_name":"Juseong Kim","orcid":"https://orcid.org/0000-0002-0576-5956"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Juseong Kim","raw_affiliation_strings":["Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032869619","display_name":"Sanghun Sel","orcid":null},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sanghun Sel","raw_affiliation_strings":["Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103125577","display_name":"Jeonghoon Choi","orcid":"https://orcid.org/0000-0002-4022-9470"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jeonghoon Choi","raw_affiliation_strings":["Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100609341","display_name":"Jae\u2010Wook Lee","orcid":"https://orcid.org/0000-0001-7142-1724"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jae-Wook Lee","raw_affiliation_strings":["Research & Development, NuclixBio, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research & Development, NuclixBio, Seoul, Republic of Korea","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023618406","display_name":"Ho Young Kang","orcid":"https://orcid.org/0000-0002-7165-1033"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ho Young Kang","raw_affiliation_strings":["Research & Development, NuclixBio, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research & Development, NuclixBio, Seoul, Republic of Korea","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012853928","display_name":"Giltae Song","orcid":"https://orcid.org/0000-0001-8796-4678"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Giltae Song","raw_affiliation_strings":["Center for Artificial Intelligence Research, Pusan National University, Busan, Republic of Korea. gsong@pusan.ac.kr","Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea. gsong@pusan.ac.kr","School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea. gsong@pusan.ac.kr","School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence Research, Pusan National University, Busan, Republic of Korea. gsong@pusan.ac.kr","institution_ids":["https://openalex.org/I4921948"]},{"raw_affiliation_string":"Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea. gsong@pusan.ac.kr","institution_ids":["https://openalex.org/I4921948"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea. gsong@pusan.ac.kr","institution_ids":["https://openalex.org/I4921948"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea","institution_ids":["https://openalex.org/I4921948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5012853928"],"corresponding_institution_ids":["https://openalex.org/I4921948"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.8297,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.97526914,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"24","issue":"1","first_page":"447","last_page":"447"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.3709999918937683,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.3709999918937683,"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"}},{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.21960000693798065,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.10480000078678131,"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/aptamer","display_name":"Aptamer","score":0.9532120823860168},{"id":"https://openalex.org/keywords/systematic-evolution-of-ligands-by-exponential-enrichment","display_name":"Systematic evolution of ligands by exponential enrichment","score":0.7297077178955078},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7153432369232178},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6998264789581299},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.614033579826355},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5393867492675781},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5010123252868652},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48994749784469604},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.477138489484787},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.47485923767089844},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4666215181350708},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4501934349536896},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39076346158981323},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3670167922973633},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23054078221321106},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.16427135467529297},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15180465579032898}],"concepts":[{"id":"https://openalex.org/C128972844","wikidata":"https://www.wikidata.org/wiki/Q418722","display_name":"Aptamer","level":2,"score":0.9532120823860168},{"id":"https://openalex.org/C122682173","wikidata":"https://www.wikidata.org/wiki/Q907101","display_name":"Systematic evolution of ligands by exponential enrichment","level":4,"score":0.7297077178955078},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7153432369232178},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6998264789581299},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.614033579826355},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5393867492675781},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5010123252868652},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48994749784469604},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.477138489484787},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.47485923767089844},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4666215181350708},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4501934349536896},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39076346158981323},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3670167922973633},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23054078221321106},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.16427135467529297},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15180465579032898},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052156","descriptor_name":"SELEX Aptamer Technique","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D052156","descriptor_name":"SELEX Aptamer Technique","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D052156","descriptor_name":"SELEX Aptamer Technique","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05577-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05577-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05577-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38012571","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38012571","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10680337","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10680337","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10680337/pdf/12859_2023_Article_5577.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:2a42a0ea0aa746b1b187a360af037ae2","is_oa":true,"landing_page_url":"https://doaj.org/article/2a42a0ea0aa746b1b187a360af037ae2","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,"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":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-20 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05577-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05577-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05577-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1478288009","display_name":null,"funder_award_id":"2021-0-02068","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G2462963976","display_name":null,"funder_award_id":"2021R1A2C2010775","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G3406192325","display_name":null,"funder_award_id":"IITP-2021-0-02068","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G4643994530","display_name":null,"funder_award_id":"2021-0-02068","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G5799620071","display_name":null,"funder_award_id":"2021-0-02068","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G6045649834","display_name":null,"funder_award_id":"IITP-2021-0-02068","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G6276415885","display_name":null,"funder_award_id":"2021R1A2C2010775","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335489","display_name":"Institute for Information and Communications Technology Promotion","ror":"https://ror.org/01g0hqq23"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389049678.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1970995363","https://openalex.org/W1991420172","https://openalex.org/W1999330037","https://openalex.org/W2000499172","https://openalex.org/W2002089022","https://openalex.org/W2006508473","https://openalex.org/W2008708467","https://openalex.org/W2025820428","https://openalex.org/W2072599666","https://openalex.org/W2079321730","https://openalex.org/W2086101556","https://openalex.org/W2092422591","https://openalex.org/W2114850508","https://openalex.org/W2130479394","https://openalex.org/W2135384038","https://openalex.org/W2135504399","https://openalex.org/W2170564629","https://openalex.org/W2410986655","https://openalex.org/W2521640490","https://openalex.org/W2547782348","https://openalex.org/W2896195439","https://openalex.org/W2921491881","https://openalex.org/W2951298881","https://openalex.org/W2970971581","https://openalex.org/W2989433860","https://openalex.org/W3017011336","https://openalex.org/W3018980093","https://openalex.org/W3033147197","https://openalex.org/W3035476925","https://openalex.org/W3038818544","https://openalex.org/W3044140833","https://openalex.org/W3093651989","https://openalex.org/W3109659125","https://openalex.org/W3127238141","https://openalex.org/W3138479300","https://openalex.org/W3160859739","https://openalex.org/W3174909509","https://openalex.org/W3177500196","https://openalex.org/W3195771950","https://openalex.org/W4220994271","https://openalex.org/W4284973298","https://openalex.org/W4285241593","https://openalex.org/W4295532582","https://openalex.org/W4308198766","https://openalex.org/W6604190760","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W4313237059","https://openalex.org/W2392306680","https://openalex.org/W4311808994","https://openalex.org/W3093450845","https://openalex.org/W4283324873","https://openalex.org/W4307216241","https://openalex.org/W3041313328","https://openalex.org/W3108749156","https://openalex.org/W4304099287","https://openalex.org/W4318203753"],"abstract_inverted_index":{"BACKGROUND:":[0],"Aptamers,":[1],"which":[2],"are":[3,58,87,148,229],"biomaterials":[4],"comprised":[5],"of":[6,26,196,216],"single-stranded":[7],"DNA/RNA":[8],"that":[9,43,185],"form":[10],"tertiary":[11,113],"structures,":[12],"have":[13,78],"significant":[14],"potential":[15],"as":[16,54,65],"next-generation":[17],"materials,":[18],"particularly":[19],"for":[20,124,150,177,190,227],"drug":[21,219],"discovery.":[22,220],"The":[23,182,221],"systematic":[24],"evolution":[25],"ligands":[27],"by":[28],"exponential":[29],"enrichment":[30],"(SELEX)":[31],"method":[32],"is":[33],"a":[34,122,157,165,174],"critical":[35],"in":[36,218],"vitro":[37],"technique":[38],"employed":[39],"to":[40,46,81,90,103,135],"identify":[41],"aptamers":[42,109],"bind":[44],"specifically":[45,88],"target":[47],"proteins.":[48],"While":[49],"advanced":[50],"SELEX-based":[51],"methods":[52,77,86,100],"such":[53,64],"Cell-":[55],"and":[56,69,110,138,193,214,224],"HT-SELEX":[57],"available,":[59],"they":[60],"often":[61,101],"encounter":[62],"issues":[63],"extended":[66],"time":[67],"consumption":[68],"suboptimal":[70],"accuracy.":[71],"Several":[72],"In":[73,116],"silico":[74],"aptamer":[75,137,179],"discovery":[76],"been":[79,162,201],"proposed":[80],"address":[82],"these":[83,99],"challenges.":[84],"These":[85],"designed":[89],"predict":[91],"aptamer-protein":[92],"interaction":[93],"(API)":[94],"using":[95,127],"benchmark":[96,158,225],"datasets.":[97],"However,":[98],"fail":[102],"consider":[104],"the":[105,142,151,194,197,212],"physicochemical":[106],"interactions":[107],"between":[108],"proteins":[111],"within":[112],"structures.":[114],"RESULTS:":[115],"this":[117],"study,":[118],"we":[119],"propose":[120],"AptaTrans,":[121],"pipeline":[123,169,199],"predicting":[125,191],"API":[126],"deep":[128],"learning":[129],"techniques.":[130],"AptaTrans":[131,160,186,198,209,228],"uses":[132],"transformer-based":[133],"encoders":[134,147],"handle":[136],"protein":[139],"sequences":[140],"at":[141,231],"monomer":[143],"level.":[144],"Furthermore,":[145],"pretrained":[146],"utilized":[149],"structural":[152],"representation.":[153],"After":[154],"validation":[155],"with":[156,172],"dataset,":[159],"has":[161,200],"integrated":[163],"into":[164],"comprehensive":[166],"toolset.":[167],"This":[168],"synergistically":[170],"combines":[171],"Apta-MCTS,":[173],"generative":[175],"algorithm":[176],"recommending":[178],"candidates.":[180],"CONCLUSION:":[181],"results":[183],"show":[184],"outperforms":[187],"existing":[188],"models":[189],"API,":[192],"efficacy":[195],"confirmed":[202],"through":[203],"various":[204],"experimental":[205],"tools.":[206],"We":[207],"expect":[208],"will":[210],"enhance":[211],"cost-effectiveness":[213],"efficiency":[215],"SELEX":[217],"source":[222],"code":[223],"dataset":[226],"available":[230],"https://github.com/pnumlb/AptaTrans":[232],".":[233]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
