{"id":"https://openalex.org/W4401806742","doi":"https://doi.org/10.1109/jbhi.2024.3448455","title":"Advancing Bioactivity Prediction Through Molecular Docking and Self-Attention","display_name":"Advancing Bioactivity Prediction Through Molecular Docking and Self-Attention","publication_year":2024,"publication_date":"2024-08-23","ids":{"openalex":"https://openalex.org/W4401806742","doi":"https://doi.org/10.1109/jbhi.2024.3448455","pmid":"https://pubmed.ncbi.nlm.nih.gov/39178096"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3448455","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3448455","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/A5026015013","display_name":"Yueming Yin","orcid":"https://orcid.org/0000-0002-9060-3248"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yueming Yin","raw_affiliation_strings":["College of Computing and Data Science, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-9060-3248","affiliations":[{"raw_affiliation_string":"College of Computing and Data Science, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091696446","display_name":"Hilbert Yuen In Lam","orcid":"https://orcid.org/0000-0001-6129-2703"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hilbert Yuen In Lam","raw_affiliation_strings":["School of Biological Sciences, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0001-6129-2703","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071286986","display_name":"Yuguang Mu","orcid":"https://orcid.org/0000-0002-2499-026X"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yuguang Mu","raw_affiliation_strings":["School of Biological Sciences, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-2499-026X","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087864456","display_name":"HY Li","orcid":"https://orcid.org/0000-0002-8603-1953"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hoi-Yeung Li","raw_affiliation_strings":["School of Biological Sciences, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-8603-1953","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047970310","display_name":"Adams Wai\u2010Kin Kong","orcid":"https://orcid.org/0000-0002-9728-9511"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Adams Wai-Kin Kong","raw_affiliation_strings":["College of Computing and Data Science, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-9728-9511","affiliations":[{"raw_affiliation_string":"College of Computing and Data Science, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":2.2631,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.89359392,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"28","issue":"12","first_page":"7599","last_page":"7610"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9955000281333923,"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":0.9955000281333923,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6006388664245605},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5871778726577759},{"id":"https://openalex.org/keywords/molecular-biophysics","display_name":"Molecular biophysics","score":0.41934627294540405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3858891427516937},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2595718801021576},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.14621767401695251},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09898245334625244}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6006388664245605},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5871778726577759},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.41934627294540405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3858891427516937},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2595718801021576},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14621767401695251},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09898245334625244},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","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":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},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2024.3448455","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3448455","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:39178096","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39178096","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":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W1585277718","https://openalex.org/W1975147762","https://openalex.org/W1979354511","https://openalex.org/W1991198394","https://openalex.org/W2015611283","https://openalex.org/W2037406737","https://openalex.org/W2056511887","https://openalex.org/W2060531713","https://openalex.org/W2085732173","https://openalex.org/W2086741044","https://openalex.org/W2096541451","https://openalex.org/W2100528947","https://openalex.org/W2108389384","https://openalex.org/W2134967712","https://openalex.org/W2142549089","https://openalex.org/W2157122545","https://openalex.org/W2290847742","https://openalex.org/W2587598315","https://openalex.org/W2620820557","https://openalex.org/W2726670313","https://openalex.org/W2739999456","https://openalex.org/W2768092025","https://openalex.org/W2890507936","https://openalex.org/W2902820054","https://openalex.org/W2907597838","https://openalex.org/W2912735973","https://openalex.org/W2930082324","https://openalex.org/W2937994991","https://openalex.org/W2968734407","https://openalex.org/W2971690404","https://openalex.org/W3007309629","https://openalex.org/W3017525988","https://openalex.org/W3100157108","https://openalex.org/W3109353507","https://openalex.org/W3109493217","https://openalex.org/W3110901318","https://openalex.org/W3128618129","https://openalex.org/W3157853087","https://openalex.org/W3162155458","https://openalex.org/W3199618438","https://openalex.org/W3202141932","https://openalex.org/W4213420837","https://openalex.org/W4220851662","https://openalex.org/W4220964139","https://openalex.org/W4281808067","https://openalex.org/W4290998851","https://openalex.org/W4294630263","https://openalex.org/W4307066870","https://openalex.org/W4313597804","https://openalex.org/W4321004126","https://openalex.org/W4360986234","https://openalex.org/W4379197245","https://openalex.org/W4381930465","https://openalex.org/W4384822685","https://openalex.org/W4385830630","https://openalex.org/W4388373766","https://openalex.org/W6675183058","https://openalex.org/W6685350579","https://openalex.org/W6726873649","https://openalex.org/W6736685754","https://openalex.org/W6754929296","https://openalex.org/W6772452955","https://openalex.org/W6838894335","https://openalex.org/W6857690643"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Bioactivity":[0],"refers":[1],"to":[2,8,124,159],"the":[3,17,51,56,73,137,140,181,187],"ability":[4],"of":[5,19,58,139,183,190,197],"a":[6,107,171],"substance":[7],"induce":[9],"biological":[10],"effects":[11],"within":[12,131],"living":[13],"systems,":[14],"often":[15],"describing":[16],"influence":[18],"molecules,":[20],"drugs,":[21],"or":[22],"chemicals":[23],"on":[24],"organisms.":[25],"In":[26],"drug":[27],"discovery,":[28],"predicting":[29],"bioactivity":[30,47,64,96,161,177,206],"streamlines":[31],"early-stage":[32],"candidate":[33],"screening":[34],"by":[35,67],"swiftly":[36],"identifying":[37],"potential":[38],"active":[39],"molecules.":[40],"The":[41],"popular":[42],"deep":[43,204],"learning":[44],"methods":[45],"in":[46,180],"prediction":[48,97,162,178,207],"primarily":[49],"model":[50],"ligand":[52,74],"structure-bioactivity":[53],"relationship":[54],"under":[55],"premise":[57],"Quantitative":[59],"Structure-Activity":[60],"Relationship":[61],"(QSAR).":[62],"However,":[63],"is":[65],"determined":[66],"multiple":[68],"factors,":[69],"including":[70],"not":[71],"only":[72],"structure":[75,150],"but":[76],"also":[77],"drug-target":[78,93],"interactions,":[79],"signaling":[80],"pathways,":[81],"reaction":[82],"environments,":[83],"pharmacokinetic":[84],"properties,":[85],"and":[86,129],"species":[87],"differences.":[88],"Our":[89],"study":[90],"first":[91],"integrates":[92],"interactions":[94],"into":[95,117],"using":[98],"protein-ligand":[99,184],"complex":[100],"data":[101,147],"from":[102,148],"molecular":[103,132],"docking.":[104],"We":[105],"devise":[106],"Drug-Target":[108],"Interaction":[109],"Graph":[110],"Neural":[111],"Network":[112],"(DTIGN),":[113],"infusing":[114],"interatomic":[115],"forces":[116],"intermolecular":[118],"graphs.":[119],"DTIGN":[120],"employs":[121],"multi-head":[122],"self-attention":[123,141],"identify":[125],"native-like":[126],"binding":[127],"pockets":[128],"poses":[130],"docking":[133],"results.":[134],"To":[135],"validate":[136],"fidelity":[138],"mechanism,":[142],"we":[143,153,169],"gather":[144],"ground":[145],"truth":[146],"crystal":[149],"databases.":[151],"Subsequently,":[152],"employ":[154],"these":[155],"limited":[156],"native":[157],"structures":[158],"refine":[160],"via":[163],"semi-supervised":[164],"learning.":[165],"For":[166],"this":[167],"study,":[168],"establish":[170],"unique":[172],"benchmark":[173],"dataset":[174],"for":[175],"evaluating":[176],"models":[179],"context":[182],"complexes,":[185],"showcasing":[186],"superior":[188],"performance":[189],"our":[191],"method":[192],"(with":[193],"an":[194],"average":[195],"improvement":[196],"27.03%)":[198],"through":[199],"comparison":[200],"with":[201],"9":[202],"leading":[203],"learning-based":[205],"methods.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
