{"id":"https://openalex.org/W4412836996","doi":"https://doi.org/10.1109/jbhi.2025.3594210","title":"Geometric Deep Learning for Protein-Ligand Affinity Prediction With Hybrid Message Passing Strategies","display_name":"Geometric Deep Learning for Protein-Ligand Affinity Prediction With Hybrid Message Passing Strategies","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4412836996","doi":"https://doi.org/10.1109/jbhi.2025.3594210","pmid":"https://pubmed.ncbi.nlm.nih.gov/40748800"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3594210","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3594210","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5057674962","display_name":"Jiaren Li","orcid":null},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaren Li","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Huasen Jiang","orcid":"https://orcid.org/0000-0003-4712-0870"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huasen Jiang","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0003-4712-0870","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083382988","display_name":"Wenjian Ma","orcid":"https://orcid.org/0000-0001-8725-1029"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjian Ma","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0001-8725-1029","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075836788","display_name":"Xiangpeng Bi","orcid":"https://orcid.org/0000-0003-4712-0870"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangpeng Bi","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043799779","display_name":"R.-S. Chen","orcid":"https://orcid.org/0000-0001-6380-4696"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Chen","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0009-0003-0115-030X","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042115840","display_name":"Weigang Lu","orcid":"https://orcid.org/0000-0002-1767-5309"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weigang Lu","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-1767-5309","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102932400","display_name":"Qing Cai","orcid":"https://orcid.org/0000-0002-8320-6156"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qing Cai","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-8320-6156","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015021852","display_name":"Fei Yang","orcid":"https://orcid.org/0000-0001-6519-7850"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Yang","raw_affiliation_strings":["School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, China"],"raw_orcid":"https://orcid.org/0000-0001-6519-7850","affiliations":[{"raw_affiliation_string":"School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101905330","display_name":"Zhiqiang Wei","orcid":"https://orcid.org/0000-0002-2774-3168"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiang Wei","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-2774-3168","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101822148","display_name":"Shugang Zhang","orcid":"https://orcid.org/0000-0002-9774-9709"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shugang Zhang","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-9774-9709","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":4.7907,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.95512801,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"30","issue":"7","first_page":"5507","last_page":"5519"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9840999841690063,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9678999781608582,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7046970129013062},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5470770597457886},{"id":"https://openalex.org/keywords/message-passing","display_name":"Message passing","score":0.45236581563949585},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3320789933204651},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.10520845651626587}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7046970129013062},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5470770597457886},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.45236581563949585},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3320789933204651},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.10520845651626587}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":"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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3594210","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3594210","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40748800","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40748800","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":"IEEE journal of biomedical and health informatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2758031463","display_name":null,"funder_award_id":"B23048","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G4770654476","display_name":null,"funder_award_id":"202561013","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7406930496","display_name":null,"funder_award_id":"202461008","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8562008206","display_name":null,"funder_award_id":"62306293","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/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1986240377","https://openalex.org/W2076779488","https://openalex.org/W2092285329","https://openalex.org/W2583907533","https://openalex.org/W2781821160","https://openalex.org/W2785947426","https://openalex.org/W2792758786","https://openalex.org/W2895884529","https://openalex.org/W2902672843","https://openalex.org/W2902812092","https://openalex.org/W2963925437","https://openalex.org/W2969996838","https://openalex.org/W2974531988","https://openalex.org/W3032123378","https://openalex.org/W3093687066","https://openalex.org/W3096561213","https://openalex.org/W3146497429","https://openalex.org/W3146944767","https://openalex.org/W3153418506","https://openalex.org/W3167575787","https://openalex.org/W3187966659","https://openalex.org/W4200139236","https://openalex.org/W4205167309","https://openalex.org/W4225405705","https://openalex.org/W4253749897","https://openalex.org/W4296311649","https://openalex.org/W4309452766","https://openalex.org/W4319999782","https://openalex.org/W4321004126","https://openalex.org/W4360986234","https://openalex.org/W4367721854","https://openalex.org/W4386084749","https://openalex.org/W4386702974","https://openalex.org/W4387068129","https://openalex.org/W4388409550","https://openalex.org/W4388571136","https://openalex.org/W4388838206","https://openalex.org/W4388939056","https://openalex.org/W4392454655","https://openalex.org/W4392811670","https://openalex.org/W4393143576","https://openalex.org/W4393305396","https://openalex.org/W4394009837","https://openalex.org/W4401610780","https://openalex.org/W4404674202","https://openalex.org/W4405440043"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1,21],"of":[2,35,123,145,174,184,191,205],"protein-ligand":[3,76],"affinity":[4,77,190],"(PLA)":[5],"is":[6],"critical":[7,54],"for":[8,19,75],"drug":[9],"discovery.":[10],"Recent":[11],"deep":[12,67],"learning":[13,23,68,83],"approaches":[14],"have":[15],"adopted":[16],"data-driven":[17],"models":[18,155],"PLA":[20],"by":[22],"intrinsic":[24],"patterns":[25],"from":[26],"one-dimensional":[27],"(1D)":[28],"sequential":[29],"or":[30],"two-dimensional":[31],"(2D)":[32],"graph":[33,82,117,122],"representations":[34],"proteins":[36],"and":[37,88,92,164,178],"ligands.":[38],"However,":[39],"these":[40],"low-dimensional":[41],"methods":[42],"overlook":[43],"the":[44,60,86,96,107,120,129,150,172,175,181,188,202,206],"three-dimensional":[45],"(3D)":[46],"geometric":[47,116],"features,":[48],"which":[49],"are":[50],"hypothesized":[51],"to":[52,84,94,104],"be":[53],"in":[55,186],"binding":[56,189],"interaction.":[57],"To":[58],"address":[59],"above":[61],"problem,":[62],"we":[63,113,170],"present":[64],"a":[65,115,139],"Geometric":[66],"approach":[69],"with":[70,99,138],"Hybrid":[71],"message":[72,111],"passing":[73],"strategies--HybridGeo,":[74],"prediction.":[78],"We":[79],"adopt":[80,114],"dual-view":[81],"model":[85,106,207],"intra-":[87],"inter-molecular":[89],"atomic":[90],"interactions":[91],"propose":[93],"aggregate":[95],"spatial":[97],"information":[98],"hybrid":[100],"strategies.":[101],"In":[102],"addition,":[103],"fully":[105],"inter-residue":[108],"dependency":[109],"upon":[110],"aggregation,":[112],"transformer":[118],"on":[119,128,156],"residue-scale":[121],"protein":[124],"pockets.":[125],"Extensive":[126],"experiments":[127],"PDBbind":[130],"dataset":[131],"show":[132],"that":[133],"HybridGeo":[134,147,185],"achieves":[135,149],"state-of-the-art":[136],"performance":[137,183],"Root":[140],"Mean":[141],"Square":[142],"Error":[143],"(RMSE)":[144],"1.172.":[146],"also":[148],"best":[151],"among":[152],"all":[153],"baseline":[154],"three":[157],"external":[158],"test":[159],"sets,":[160],"showcasing":[161],"good":[162],"generalizability":[163],"robustness.":[165],"Through":[166],"systematic":[167],"ablation":[168],"experiments,":[169],"validated":[171],"effectiveness":[173],"proposed":[176],"modules,":[177],"further":[179,200],"demonstrated":[180],"superior":[182],"predicting":[187],"macrocyclic":[192],"compound":[193],"complexes":[194],"through":[195],"case":[196],"studies.":[197],"Visualization":[198],"analysis":[199],"indicates":[201],"biological":[203],"interpretability":[204],"predictions.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
