{"id":"https://openalex.org/W7126014005","doi":"https://doi.org/10.1109/bibm66473.2025.11356765","title":"Agnostic Biomolecular Binding Affinity Prediction via Frame Averaging Graph Transformer","display_name":"Agnostic Biomolecular Binding Affinity Prediction via Frame Averaging Graph Transformer","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126014005","doi":"https://doi.org/10.1109/bibm66473.2025.11356765"},"language":"en","primary_location":{"id":"doi:10.1109/bibm66473.2025.11356765","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356765","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":"conference-paper","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/A5120413896","display_name":"Krinos Li","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Krinos Li","raw_affiliation_strings":["Imperial College London,Department of Bioengineering & Imperial-X,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Imperial College London,Department of Bioengineering & Imperial-X,UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124276472","display_name":"Lucas He","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139815","display_name":"MRC Unit for Lifelong Health and Ageing","ror":"https://ror.org/03kpvby98","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210087105","https://openalex.org/I4210139815","https://openalex.org/I45129253","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lucas He","raw_affiliation_strings":["Unit for Lifelong Health and Ageing at UCL, UCL Hawkes Institute, University College London,Department of Computer Science,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unit for Lifelong Health and Ageing at UCL, UCL Hawkes Institute, University College London,Department of Computer Science,UK","institution_ids":["https://openalex.org/I4210139815","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088846231","display_name":"Xianglu Xiao","orcid":"https://orcid.org/0000-0002-8648-6245"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Xianglu Xiao","raw_affiliation_strings":["Imperial College London,Department of Bioengineering & Imperial-X,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Imperial College London,Department of Bioengineering & Imperial-X,UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Shenglong Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shenglong Deng","raw_affiliation_strings":["Imperial College London,Department of Bioengineering & Imperial-X,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Imperial College London,Department of Bioengineering & Imperial-X,UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124200583","display_name":"Zijun Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139815","display_name":"MRC Unit for Lifelong Health and Ageing","ror":"https://ror.org/03kpvby98","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210087105","https://openalex.org/I4210139815","https://openalex.org/I45129253","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zijun Zhong","raw_affiliation_strings":["Unit for Lifelong Health and Ageing at UCL, UCL Hawkes Institute, University College London,Department of Computer Science,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unit for Lifelong Health and Ageing at UCL, UCL Hawkes Institute, University College London,Department of Computer Science,UK","institution_ids":["https://openalex.org/I4210139815","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124230113","display_name":"Yue Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Yue Yang","raw_affiliation_strings":["Imperial College London,Department of Bioengineering & Imperial-X,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Imperial College London,Department of Bioengineering & Imperial-X,UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124171570","display_name":"Guang Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Guang Yang","raw_affiliation_strings":["Imperial College London,Department of Bioengineering & Imperial-X,UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Imperial College London,Department of Bioengineering & Imperial-X,UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.66978883,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"787","last_page":"792"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6328999996185303,"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":0.6328999996185303,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.15950000286102295,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.0828000009059906,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.6121000051498413},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5536999702453613},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5073999762535095},{"id":"https://openalex.org/keywords/frame","display_name":"Frame (networking)","score":0.39480000734329224},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.32190001010894775}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7062000036239624},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.6121000051498413},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5536999702453613},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5073999762535095},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4230000078678131},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.39480000734329224},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37529999017715454},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36489999294281006},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3441999852657318},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.32190001010894775},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.3012999892234802},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.25529998540878296}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356765","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356765","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"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10220997","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10220997/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"In: 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). (pp. pp. 787-792). IEEE: Wuhan, China. (2026)","raw_type":"Proceedings paper"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1251990094","display_name":null,"funder_award_id":"RDA01","funder_id":"https://openalex.org/F4320336039","funder_display_name":"NIHR Imperial Biomedical Research Centre"},{"id":"https://openalex.org/G1285418384","display_name":null,"funder_award_id":"IECNSFC211235","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G1744717256","display_name":null,"funder_award_id":"MC/PC/21013","funder_id":"https://openalex.org/F4320334321","funder_display_name":"Musculoskeletal Research Center, Washington University in St. Louis"},{"id":"https://openalex.org/G7777866522","display_name":null,"funder_award_id":"MR/U506710/1","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320334321","display_name":"Musculoskeletal Research Center, Washington University in St. Louis","ror":null},{"id":"https://openalex.org/F4320336039","display_name":"NIHR Imperial Biomedical Research Centre","ror":"https://ror.org/01kmhx639"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W175253381","https://openalex.org/W1500036797","https://openalex.org/W1915490970","https://openalex.org/W1986240377","https://openalex.org/W1993046136","https://openalex.org/W2062632020","https://openalex.org/W2785947426","https://openalex.org/W2892745578","https://openalex.org/W2939052792","https://openalex.org/W2973114758","https://openalex.org/W2984726926","https://openalex.org/W3087769169","https://openalex.org/W3168436232","https://openalex.org/W3182055317","https://openalex.org/W3187966659","https://openalex.org/W4281742422","https://openalex.org/W4362663312","https://openalex.org/W4391542588","https://openalex.org/W4401340626","https://openalex.org/W4402623547","https://openalex.org/W4404505690","https://openalex.org/W4409346604","https://openalex.org/W4409906723"],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"binding":[1,84],"affinity":[2,85],"between":[3],"biomolecules":[4],"is":[5,49],"a":[6,43,60],"critical":[7],"task":[8],"in":[9,55],"drug":[10],"discovery,":[11],"where":[12],"deep":[13],"learning":[14],"methods":[15],"have":[16],"achieved":[17],"significant":[18],"progress.":[19],"However,":[20],"many":[21],"existing":[22],"approaches":[23],"employ":[24],"modality-specific":[25],"network":[26],"architectures,":[27],"limiting":[28],"their":[29],"direct":[30],"applicability":[31,109],"across":[32,112],"diverse":[33],"biomolecular":[34,52,114],"interaction":[35,53,115],"types.":[36,116],"In":[37],"this":[38],"work,":[39],"we":[40],"propose":[41],"F3Affinity,":[42],"novel":[44],"structure-based":[45],"graph":[46],"transformer":[47],"that":[48,76],"agnostic":[50],"to":[51,82],"type":[54],"its":[56,107],"architectural":[57],"design.":[58],"Leveraging":[59],"frame":[61],"averaging":[62],"technique,":[63],"our":[64],"model":[65],"flexibly":[66],"learns":[67],"SE(3)-invariant":[68],"representations":[69],"of":[70],"input":[71],"structures.":[72],"We":[73],"further":[74],"demonstrate":[75],"F3Affinity":[77],"can":[78],"be":[79],"independently":[80],"applied":[81],"various":[83],"prediction":[86],"benchmarks":[87],"without":[88],"requiring":[89],"any":[90],"pre-trained":[91],"embeddings,":[92],"including":[93],"protein-ligand,":[94],"protein-protein,":[95],"and":[96,100,110],"protein-nucleic":[97],"acid":[98],"interactions,":[99],"achieving":[101],"competitive":[102],"performance.":[103],"These":[104],"results":[105],"validate":[106],"broad":[108],"effectiveness":[111],"multiple":[113]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2026-01-30T00:00:00"}