{"id":"https://openalex.org/W7126054664","doi":"https://doi.org/10.1109/bibm66473.2025.11356162","title":"ASRSMA: Atomic-Scale and Structure-Based Modeling for RNA-Small Molecule Binding Affinity Prediction via Contrastive Pretraining","display_name":"ASRSMA: Atomic-Scale and Structure-Based Modeling for RNA-Small Molecule Binding Affinity Prediction via Contrastive Pretraining","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126054664","doi":"https://doi.org/10.1109/bibm66473.2025.11356162"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356162","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356162","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069593314","display_name":"Yong Li","orcid":"https://orcid.org/0000-0003-4038-0493"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yahan Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University,Changsha,China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124195512","display_name":"Zhijian Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijian Huang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University,Changsha,China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124194028","display_name":"Song Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Song Chen","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University,Changsha,China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010717360","display_name":"Yucheng Wang","orcid":"https://orcid.org/0000-0002-7755-228X"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yucheng Wang","raw_affiliation_strings":["Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR),Singapore"],"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR),Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123451689","display_name":"M. Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Min Wu","raw_affiliation_strings":["Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR),Singapore"],"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR),Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124164099","display_name":"Lei Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Deng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University,Changsha,China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5069593314"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.65166392,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"154","last_page":"157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.5245000123977661,"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":0.5245000123977661,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.24629999697208405,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.06129999831318855,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5522000193595886},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48249998688697815},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.47589999437332153},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4287000000476837},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.41100001335144043},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.3628000020980835},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.3587999939918518},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.34439998865127563}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.59579998254776},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5522000193595886},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5360000133514404},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48249998688697815},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.47589999437332153},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44339999556541443},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4287000000476837},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4239000082015991},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.41100001335144043},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.3628000020980835},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.36090001463890076},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.3587999939918518},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.34439998865127563},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.33799999952316284},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.3133000135421753},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.2939999997615814},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.2865999937057495},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.27570000290870667},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27309998869895935},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2639999985694885},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.25440001487731934}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356162","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356162","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6419755262","display_name":null,"funder_award_id":"2025JJ20062","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G6623812488","display_name":null,"funder_award_id":"U23A20321,62272490","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1993046136","https://openalex.org/W2124241917","https://openalex.org/W2442594675","https://openalex.org/W2784213390","https://openalex.org/W2820941669","https://openalex.org/W2883929619","https://openalex.org/W3013781651","https://openalex.org/W4385245566","https://openalex.org/W4391132552","https://openalex.org/W4393055202","https://openalex.org/W4404377730","https://openalex.org/W4406942799","https://openalex.org/W4414422336"],"related_works":[],"abstract_inverted_index":{"RNA":[0,77],"is":[1,44,115],"intricately":[2],"involved":[3],"in":[4,18,153],"aberrant":[5],"cellular":[6],"functions":[7],"and":[8,23,78,97,105],"a":[9,31,110],"wide":[10],"range":[11],"of":[12,40,87,125],"disease":[13],"processes,":[14],"playing":[15],"pivotal":[16],"roles":[17],"gene":[19],"regulation,":[20],"viral":[21],"replication,":[22],"innate":[24],"immunity.":[25],"Consequently,":[26],"it":[27,43],"has":[28],"emerged":[29],"as":[30,61],"highly":[32],"promising":[33],"therapeutic":[34],"target.":[35],"To":[36],"accelerate":[37],"the":[38,85,120,126],"discovery":[39],"such":[41],"drugs,":[42],"essential":[45],"to":[46,102],"develop":[47],"an":[48,62,93,98],"effective":[49],"computational":[50],"method":[51],"for":[52,69],"predicting":[53,154],"RNA-small":[54,70,155],"molecule":[55,71,156],"affinity.":[56],"Therefore,":[57],"we":[58],"propose":[59],"ASRSMA":[60,75,147],"atomiclevel":[63],"structure-aware":[64],"model":[65,103],"with":[66,139],"contrastive":[67,112],"pre-training":[68],"binding":[72,157],"affinity":[73],"prediction.":[74],"represents":[76],"small":[79],"molecules":[80],"at":[81],"atomic":[82],"resolution,":[83],"enabling":[84],"capture":[86],"fine-grained":[88],"structural":[89],"features.":[90],"It":[91],"incorporates":[92],"atom-pair":[94],"encoding":[95],"module":[96,101],"inter-molecular":[99,106],"interaction":[100],"intra-":[104],"interactions.":[107],"In":[108],"addition,":[109],"self-supervised":[111],"learning":[113],"strategy":[114],"employed":[116],"during":[117],"pre-training,":[118],"maximising":[119],"similarity":[121],"between":[122],"different":[123,133],"views":[124],"same":[127],"complex":[128],"while":[129],"minimising":[130],"similarities":[131],"across":[132],"complexes,":[134],"thereby":[135],"yielding":[136],"deep":[137],"representations":[138],"strong":[140],"generalisation":[141],"capacity.":[142],"Experimental":[143],"results":[144],"demonstrate":[145],"that":[146],"significantly":[148],"outperforms":[149],"state-of-the-art":[150],"baseline":[151],"models":[152],"affinities.":[158]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}