{"id":"https://openalex.org/W4389257854","doi":"https://doi.org/10.1093/bib/bbad435","title":"KGDiff: towards explainable target-aware molecule generation with knowledge guidance","display_name":"KGDiff: towards explainable target-aware molecule generation with knowledge guidance","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4389257854","doi":"https://doi.org/10.1093/bib/bbad435","pmid":"https://pubmed.ncbi.nlm.nih.gov/38040493"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad435","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad435/55464687/bbad435.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad435/55464687/bbad435.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102404029","display_name":"Hao Qian","orcid":"https://orcid.org/0009-0001-7071-3685"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210151021","display_name":"Shanghai Institute of Computing Technology","ror":"https://ror.org/05ek0ze18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210151021"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Qian","raw_affiliation_strings":["Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","Department of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210151021"]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060074967","display_name":"Wenjing Huang","orcid":"https://orcid.org/0000-0001-7001-6516"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210151021","display_name":"Shanghai Institute of Computing Technology","ror":"https://ror.org/05ek0ze18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210151021"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjing Huang","raw_affiliation_strings":["Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","Department of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210151021"]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073963268","display_name":"Shikui Tu","orcid":"https://orcid.org/0000-0001-6270-0449"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210151021","display_name":"Shanghai Institute of Computing Technology","ror":"https://ror.org/05ek0ze18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210151021"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shikui Tu","raw_affiliation_strings":["Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","Department of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210151021"]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069972085","display_name":"Lei Xu","orcid":"https://orcid.org/0000-0002-2752-1573"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210151021","display_name":"Shanghai Institute of Computing Technology","ror":"https://ror.org/05ek0ze18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210151021"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lei Xu","raw_affiliation_strings":["Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","Department of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240 , China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210151021"]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5069972085","https://openalex.org/A5073963268"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210151021"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.8859,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.94940541,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9904000163078308,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9793000221252441,"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/computer-science","display_name":"Computer science","score":0.502140998840332}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.502140998840332}],"mesh":[{"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":"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":"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":"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":"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":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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad435","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad435/55464687/bbad435.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38040493","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38040493","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10783868","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10783868","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10783868/pdf/bbad435.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad435","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad435/55464687/bbad435.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2415283116","display_name":null,"funder_award_id":"62172273","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8721642152","display_name":null,"funder_award_id":"2021SHZDZX0102","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"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389257854.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1975447903","https://openalex.org/W2104477830","https://openalex.org/W2134967712","https://openalex.org/W2151697120","https://openalex.org/W2756953478","https://openalex.org/W2913668833","https://openalex.org/W2948831670","https://openalex.org/W3019745511","https://openalex.org/W3028589594","https://openalex.org/W3082411326","https://openalex.org/W3085029011","https://openalex.org/W3119872582","https://openalex.org/W3151148247","https://openalex.org/W3162926177","https://openalex.org/W4200139236","https://openalex.org/W4221138292","https://openalex.org/W4226226115","https://openalex.org/W4303431765","https://openalex.org/W4307416138","https://openalex.org/W4309101307","https://openalex.org/W4309679168","https://openalex.org/W4309801650","https://openalex.org/W4378071155","https://openalex.org/W4380739447","https://openalex.org/W6679045638","https://openalex.org/W6682196880","https://openalex.org/W6795288823","https://openalex.org/W6804214328","https://openalex.org/W6810653082","https://openalex.org/W6838000958","https://openalex.org/W6846341140","https://openalex.org/W6846936329","https://openalex.org/W6850636830"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032"],"abstract_inverted_index":{"Designing":[0],"3D":[1,28],"molecules":[2,24,48,73,194],"with":[3,83,133,200],"high":[4,84,114],"binding":[5,53,95,115],"affinity":[6,96],"for":[7],"specific":[8],"protein":[9,81],"targets":[10],"is":[11,18,122,141,155,195],"crucial":[12],"in":[13,27],"drug":[14],"design.":[15],"One":[16],"challenge":[17],"that":[19,74],"the":[20,37,43,47,52,90,98,103,107,111,126,134,138,149,170,173,178,182,192,198,201],"atomic":[21],"interaction":[22],"between":[23,46,55],"and":[25,49,101,130,143,162,197],"proteins":[26],"space":[29],"has":[30],"to":[31,59,71,78,105,124,148],"be":[32,76],"taken":[33],"into":[34,97],"account.":[35],"However,":[36],"existing":[38],"target-aware":[39],"methods":[40],"solely":[41],"model":[42,70],"joint":[44],"distribution":[45],"proteins,":[50],"disregarding":[51],"affinities":[54],"them,":[56],"which":[57],"leads":[58],"limited":[60],"performance.":[61],"In":[62],"this":[63],"paper,":[64],"we":[65],"propose":[66],"an":[67,118,188],"explainable":[68],"diffusion":[69,99],"generate":[72],"can":[75],"bound":[77],"a":[79],"given":[80],"target":[82],"affinity.":[85,116],"Our":[86],"method":[87],"explicitly":[88],"incorporates":[89],"chemical":[91],"knowledge":[92,104,140,203],"of":[93,113,169,172,184,191],"protein-ligand":[94],"model,":[100],"uses":[102],"guide":[106],"denoising":[108,135],"process":[109],"towards":[110],"direction":[112],"Specifically,":[117],"SE(3)-invariant":[119],"expert":[120,150,174],"network":[121],"developed":[123],"fit":[125],"Vina":[127,146],"scoring":[128],"functions":[129,147],"jointly":[131],"trained":[132],"network,":[136],"while":[137],"domain":[139,202],"distilled":[142],"conveyed":[144],"from":[145],"network.":[151,175],"An":[152],"effective":[153],"guidance":[154],"proposed":[156],"on":[157,177],"both":[158],"continuous":[159],"atom":[160,164],"coordinates":[161],"discrete":[163],"types":[165],"by":[166],"taking":[167],"advantages":[168],"gradient":[171],"Experiments":[176],"benchmark":[179],"CrossDocked2020":[180],"demonstrate":[181],"superiority":[183],"our":[185],"method.":[186],"Additionally,":[187],"atom-level":[189],"explanation":[190],"generated":[193],"provided,":[196],"connections":[199],"are":[204],"established.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":7}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
