{"id":"https://openalex.org/W4387068129","doi":"https://doi.org/10.1109/tnnls.2023.3314928","title":"Structure-Aware Graph Attention Diffusion Network for Protein\u2013Ligand Binding Affinity Prediction","display_name":"Structure-Aware Graph Attention Diffusion Network for Protein\u2013Ligand Binding Affinity Prediction","publication_year":2023,"publication_date":"2023-09-26","ids":{"openalex":"https://openalex.org/W4387068129","doi":"https://doi.org/10.1109/tnnls.2023.3314928","pmid":"https://pubmed.ncbi.nlm.nih.gov/37751351"},"language":"en","primary_location":{"id":"doi:10.1109/tnnls.2023.3314928","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tnnls.2023.3314928","pdf_url":null,"source":{"id":"https://openalex.org/S4210175523","display_name":"IEEE Transactions on Neural Networks and Learning Systems","issn_l":"2162-237X","issn":["2162-237X","2162-2388"],"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 Transactions on Neural Networks and Learning Systems","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/A5100745804","display_name":"Li Mei","orcid":"https://orcid.org/0000-0002-9361-7231"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mei Li","raw_affiliation_strings":["Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","College of Computer Science, Tianjin Key Laboratory of Network and Data Security Technology, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0002-9361-7231","affiliations":[{"raw_affiliation_string":"Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"College of Computer Science, Tianjin Key Laboratory of Network and Data Security Technology, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007223036","display_name":"Ye Cao","orcid":"https://orcid.org/0000-0002-3725-4536"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ye Cao","raw_affiliation_strings":["Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0002-3725-4536","affiliations":[{"raw_affiliation_string":"Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390120","display_name":"Xiaoguang Liu","orcid":"https://orcid.org/0000-0002-9010-3278"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoguang Liu","raw_affiliation_strings":["Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","College of Computer Science, Tianjin Key Laboratory of Network and Data Security Technology, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0002-9010-3278","affiliations":[{"raw_affiliation_string":"Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"College of Computer Science, Tianjin Key Laboratory of Network and Data Security Technology, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059824709","display_name":"Hua Ji","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Ji","raw_affiliation_strings":["Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","College of Computer Science, Tianjin Key Laboratory of Network and Data Security Technology, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tianjin Key Laboratory of Network and Data Security Technology, College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"College of Computer Science, Tianjin Key Laboratory of Network and Data Security Technology, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":null,"apc_paid":null,"fwci":3.2817,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.93521156,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"12","first_page":"18370","last_page":"18380"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9987000226974487,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.996399998664856,"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/ligand","display_name":"Ligand (biochemistry)","score":0.4454803168773651},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4303463101387024},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43028131127357483},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4112223982810974},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3899471163749695},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20980051159858704},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1846596598625183},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1733589768409729},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.14034414291381836}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4454803168773651},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4303463101387024},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43028131127357483},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4112223982810974},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3899471163749695},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20980051159858704},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1846596598625183},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1733589768409729},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.14034414291381836}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","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":"D006801","descriptor_name":"Humans","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":"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":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tnnls.2023.3314928","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tnnls.2023.3314928","pdf_url":null,"source":{"id":"https://openalex.org/S4210175523","display_name":"IEEE Transactions on Neural Networks and Learning Systems","issn_l":"2162-237X","issn":["2162-237X","2162-2388"],"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 Transactions on Neural Networks and Learning Systems","raw_type":"journal-article"},{"id":"pmid:37751351","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37751351","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 transactions on neural networks and learning systems","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1454563993","display_name":null,"funder_award_id":"62272253","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7931203216","display_name":null,"funder_award_id":"62272252","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/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W2047509756","https://openalex.org/W2067732724","https://openalex.org/W2109991441","https://openalex.org/W2134967712","https://openalex.org/W2148512505","https://openalex.org/W2194775991","https://openalex.org/W2214665483","https://openalex.org/W2587598315","https://openalex.org/W2781821160","https://openalex.org/W2894175828","https://openalex.org/W2902812092","https://openalex.org/W2963833291","https://openalex.org/W2969996838","https://openalex.org/W2974531988","https://openalex.org/W2984249386","https://openalex.org/W2998496395","https://openalex.org/W3005043246","https://openalex.org/W3018980093","https://openalex.org/W3033050543","https://openalex.org/W3096561213","https://openalex.org/W3098189759","https://openalex.org/W3098846260","https://openalex.org/W3109549311","https://openalex.org/W3112527819","https://openalex.org/W3140330522","https://openalex.org/W3157078379","https://openalex.org/W3158144848","https://openalex.org/W3167575787","https://openalex.org/W3171389163","https://openalex.org/W3177828909","https://openalex.org/W3200409365","https://openalex.org/W4200139236","https://openalex.org/W4200432496","https://openalex.org/W4206488367","https://openalex.org/W4212815277","https://openalex.org/W4213077304","https://openalex.org/W4221095602","https://openalex.org/W4221146126","https://openalex.org/W4225907994","https://openalex.org/W4251512373","https://openalex.org/W4282827695","https://openalex.org/W4290877452","https://openalex.org/W4296311649","https://openalex.org/W4306317360","https://openalex.org/W4323338513","https://openalex.org/W6688357764","https://openalex.org/W6726873649","https://openalex.org/W6736685754","https://openalex.org/W6738964360","https://openalex.org/W6753331806","https://openalex.org/W6757634740","https://openalex.org/W6760001035","https://openalex.org/W6761665040","https://openalex.org/W6787484091","https://openalex.org/W6809736655","https://openalex.org/W6810689541"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1],"of":[2,11,22,36,46,52,148],"protein-ligand":[3,23],"binding":[4,58,151],"affinities":[5],"can":[6],"significantly":[7],"advance":[8],"the":[9,44,66,134,146],"development":[10],"drug":[12],"discovery.":[13],"Several":[14],"graph":[15,68,105],"neural":[16],"network":[17,71],"(GNN)-based":[18],"methods":[19,40],"learn":[20,49],"representations":[21],"complexes":[24,87],"via":[25],"modeling":[26],"intermolecule":[27],"interactions":[28,118],"and":[29,34,48,77,93,119],"spatial":[30,82,121],"structures":[31,51,136],"(e.g.,":[32],"distances":[33],"angles)":[35],"complexes.":[37,138],"However,":[38],"these":[39],"fail":[41],"to":[42,73,113,132],"emphasize":[43],"importance":[45],"bonds":[47,98],"hierarchical":[50,135],"complexes,":[53],"which":[54],"are":[55],"significant":[56],"for":[57,80,150],"affinity":[59,152],"prediction.":[60,153],"In":[61],"this":[62],"article,":[63],"we":[64,102,125],"propose":[65,126],"structure-aware":[67],"attention":[69,106],"diffusion":[70,107],"(SGADN)":[72],"incorporate":[74],"both":[75],"distance":[76,92],"angle":[78,94],"information":[79],"efficient":[81],"structure":[83,122],"learning.":[84,123],"We":[85],"model":[86],"as":[88,99],"line":[89,104,111],"graphs":[90,112],"with":[91],"information,":[95],"focusing":[96],"on":[97,110,142],"nodes.":[100],"Then":[101],"perform":[103],"layers":[108],"(LGADLs)":[109],"explore":[114],"long-range":[115],"bond":[116],"node":[117],"enhance":[120],"Furthermore,":[124],"an":[127],"attentive":[128],"pooling":[129],"layer":[130],"(APL)":[131],"refine":[133],"in":[137],"Extensive":[139],"experimental":[140],"studies":[141],"two":[143],"benchmarks":[144],"demonstrate":[145],"superiority":[147],"SGADN":[149]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
