{"id":"https://openalex.org/W4404035653","doi":"https://doi.org/10.1109/jbhi.2024.3491318","title":"Equivariant 3D-Conditional Diffusion Model for <i>De Novo</i> Drug Design","display_name":"Equivariant 3D-Conditional Diffusion Model for <i>De Novo</i> Drug Design","publication_year":2024,"publication_date":"2024-11-04","ids":{"openalex":"https://openalex.org/W4404035653","doi":"https://doi.org/10.1109/jbhi.2024.3491318","pmid":"https://pubmed.ncbi.nlm.nih.gov/39495691"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3491318","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3491318","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/A5010594849","display_name":"Zheng Jia","orcid":"https://orcid.org/0000-0001-8459-515X"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia Zheng","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi&#x0027;an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi&#x0027;an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102010573","display_name":"Hai-Cheng Yi","orcid":"https://orcid.org/0000-0001-8339-396X"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hai-Cheng Yi","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi&#x0027;an, China"],"raw_orcid":"https://orcid.org/0000-0001-8339-396X","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi&#x0027;an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019805735","display_name":"Zhu\u2010Hong You","orcid":"https://orcid.org/0000-0003-1266-2696"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhu-Hong You","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi&#x0027;an, China"],"raw_orcid":"https://orcid.org/0000-0003-1266-2696","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi&#x0027;an, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":null,"apc_paid":null,"fwci":3.0029,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.92000558,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"29","issue":"3","first_page":"1805","last_page":"1816"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12270","display_name":"Microwave-Assisted Synthesis and Applications","score":0.6439999938011169,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12270","display_name":"Microwave-Assisted Synthesis and Applications","score":0.6439999938011169,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12080","display_name":"Injection Molding Process and Properties","score":0.5866000056266785,"subfield":{"id":"https://openalex.org/subfields/2210","display_name":"Mechanical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13791","display_name":"Veterinary medicine and infectious diseases","score":0.5636000037193298,"subfield":{"id":"https://openalex.org/subfields/3404","display_name":"Small Animals"},"field":{"id":"https://openalex.org/fields/34","display_name":"Veterinary"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6181886196136475},{"id":"https://openalex.org/keywords/equivariant-map","display_name":"Equivariant map","score":0.5164259076118469},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.45302459597587585},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4089944064617157},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3568263053894043},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34013664722442627},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25009703636169434},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14041852951049805},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.13242259621620178}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6181886196136475},{"id":"https://openalex.org/C171036898","wikidata":"https://www.wikidata.org/wiki/Q256355","display_name":"Equivariant map","level":2,"score":0.5164259076118469},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.45302459597587585},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4089944064617157},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3568263053894043},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34013664722442627},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25009703636169434},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14041852951049805},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.13242259621620178},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"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":"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":"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2024.3491318","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3491318","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:39495691","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39495691","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":[{"id":"https://openalex.org/G1155641646","display_name":null,"funder_award_id":"D5000230193","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3639475604","display_name":null,"funder_award_id":"62325308","funder_id":"https://openalex.org/F4320336125","funder_display_name":"National Science Fund for Distinguished Young Scholars"}],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320336125","display_name":"National Science Fund for Distinguished Young Scholars","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1596185498","https://openalex.org/W1951102280","https://openalex.org/W1977556410","https://openalex.org/W2012949016","https://openalex.org/W2031441006","https://openalex.org/W2047112187","https://openalex.org/W2052933929","https://openalex.org/W2108389384","https://openalex.org/W2146465875","https://openalex.org/W2160592148","https://openalex.org/W2169678694","https://openalex.org/W2273267066","https://openalex.org/W2594726310","https://openalex.org/W2806834952","https://openalex.org/W2971690404","https://openalex.org/W3009999522","https://openalex.org/W3082411326","https://openalex.org/W3125566655","https://openalex.org/W3127493072","https://openalex.org/W3174777205","https://openalex.org/W3209764902","https://openalex.org/W3217546525","https://openalex.org/W4248107770","https://openalex.org/W4280562526","https://openalex.org/W4309842604","https://openalex.org/W4309884249","https://openalex.org/W4321254242","https://openalex.org/W4367049415","https://openalex.org/W4379967792","https://openalex.org/W4386498912","https://openalex.org/W4386898749","https://openalex.org/W4389937842","https://openalex.org/W4390832808","https://openalex.org/W4394718179","https://openalex.org/W4404995526","https://openalex.org/W4405194591","https://openalex.org/W6678914141","https://openalex.org/W6684578312","https://openalex.org/W6693372400","https://openalex.org/W6774736260","https://openalex.org/W6779823529","https://openalex.org/W6790561777","https://openalex.org/W6796163713","https://openalex.org/W6797906067","https://openalex.org/W6804214328","https://openalex.org/W6810438242","https://openalex.org/W6810653082","https://openalex.org/W6838000958","https://openalex.org/W6849883715","https://openalex.org/W6850636830","https://openalex.org/W6862998299"],"related_works":["https://openalex.org/W3148895720","https://openalex.org/W2393913406","https://openalex.org/W2356579025","https://openalex.org/W2736697936","https://openalex.org/W3211835374","https://openalex.org/W30258475","https://openalex.org/W2548611373","https://openalex.org/W1601809778","https://openalex.org/W3169304289","https://openalex.org/W2373733345"],"abstract_inverted_index":{"De":[0],"novo":[1],"drug":[2,6],"design":[3],"speeds":[4],"up":[5],"discovery,":[7],"mitigating":[8],"its":[9],"time":[10,116],"and":[11,113,143],"cost":[12],"burdens":[13],"with":[14,40,130,145],"advanced":[15],"computational":[16,111],"methods.":[17],"Previous":[18],"work":[19],"either":[20],"insufficiently":[21],"utilized":[22],"the":[23,28,70,150],"3D":[24,60],"geometric":[25,61,73],"structure":[26],"of":[27,63,72,80],"target":[29,65],"proteins,":[30],"or":[31],"generated":[32],"ligands":[33,129],"in":[34,127],"an":[35,46,86],"order":[36],"that":[37],"was":[38],"inconsistent":[39],"real":[41],"physics.":[42],"Here":[43],"we":[44,92],"propose":[45],"equivariant":[47,87],"3D-conditional":[48],"diffusion":[49,95],"model,":[50],"named":[51],"DiffFBDD,":[52],"for":[53,104,148],"generating":[54,101,128],"new":[55],"pharmaceutical":[56],"compounds":[57],"based":[58],"on":[59],"information":[62,74,79],"specific":[64,105,135],"protein":[66,106,136],"pockets.":[67],"DiffFBDD":[68,120],"overcomes":[69],"underutilization":[71],"by":[75,100],"integrating":[76],"full":[77],"atomic":[78],"pockets":[81],"to":[82,97,134],"backbone":[83],"atoms":[84],"using":[85],"graph":[88],"neural":[89],"network.":[90],"Moreover,":[91],"develop":[93],"a":[94],"approach":[96],"generate":[98],"drugs":[99],"ligand":[102],"fragments":[103],"pockets,":[107,137],"which":[108],"requires":[109],"fewer":[110],"resources":[112],"less":[114],"generation":[115],"(65.98%":[117],"96.10%":[118],"lower).":[119],"offers":[121],"better":[122],"performance":[123],"than":[124],"state-of-the-art":[125],"models":[126],"strong":[131],"binding":[132],"affinity":[133],"while":[138],"maintaining":[139],"high":[140],"validity,":[141],"uniqueness,":[142],"novelty,":[144],"clear":[146],"potential":[147],"exploring":[149],"drug-like":[151],"chemical":[152],"space.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2024-11-05T00:00:00"}
