{"id":"https://openalex.org/W4415201053","doi":"https://doi.org/10.1021/acs.jcim.6c01046","title":"Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design","display_name":"Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design","publication_year":2026,"publication_date":"2026-10-27","ids":{"openalex":"https://openalex.org/W4415201053","doi":"https://doi.org/10.1021/acs.jcim.6c01046"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6c01046","doi":"https://doi.org/10.1021/acs.jcim.6c01046","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01046","pdf_url":"https://pubs.acs.org/jcisd8/article-pdf/doi/10.1021/acs.jcim.6c01046/68986526/acs.jcim.6c01046.pdf","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/jcisd8/article-pdf/doi/10.1021/acs.jcim.6c01046/68986526/acs.jcim.6c01046.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020216708","display_name":"Amira A. Alakhdar","orcid":"https://orcid.org/0009-0008-1419-9467","observed_orcids":["https://orcid.org/0009-0008-1419-9467"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amira Alakhdar","raw_affiliation_strings":["Carnegie Mellon University , , , ,"],"raw_orcid":"https://orcid.org/0009-0008-1419-9467","affiliations":[{"raw_affiliation_string":"Carnegie Mellon University , , , ,","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013695358","display_name":"Barnab\u00e1s P\u00f3czos","orcid":"https://orcid.org/0000-0002-2898-4705","observed_orcids":["https://orcid.org/0000-0002-2898-4705"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barnabas Poczos","raw_affiliation_strings":["Carnegie Mellon University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University , , , ,","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067949293","display_name":"Newell R. Washburn","orcid":"https://orcid.org/0000-0001-7843-8860","observed_orcids":["https://orcid.org/0000-0001-7843-8860"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Newell Washburn","raw_affiliation_strings":["Carnegie Mellon University , , , ,"],"raw_orcid":"https://orcid.org/0000-0001-7843-8860","affiliations":[{"raw_affiliation_string":"Carnegie Mellon University , , , ,","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":null,"display_name":"Kevin Cusack","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2948539688","display_name":"AbbVie (United States)","ror":"https://ror.org/02g5p4n58","country_code":"US","type":"company","lineage":["https://openalex.org/I2948539688"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Cusack","raw_affiliation_strings":["AbbVie Bioresearch Center , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AbbVie Bioresearch Center , , ,","institution_ids":["https://openalex.org/I2948539688"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067949293"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":{"value":4500,"currency":"USD","value_usd":4500},"fwci":5.3588,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.95014428,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":97},"biblio":{"volume":null,"issue":null,"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":1.0,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.0,"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/T14099","display_name":"Synthesis and Characterization of Heterocyclic Compounds","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/ligand-based-drug-design","display_name":"ligand-based drug design","score":0.7239999771118164},{"id":"https://openalex.org/keywords/de-novo-drug-design","display_name":"de novo drug design","score":0.9120000004768372},{"id":"https://openalex.org/keywords/3d-molecular-generation","display_name":"3D molecular generation","score":0.9039999842643738},{"id":"https://openalex.org/keywords/pharmacophore-modeling","display_name":"pharmacophore modeling","score":0.7419999837875366},{"id":"https://openalex.org/keywords/transformer-based-generative-models","display_name":"transformer-based generative models","score":0.5630000233650208},{"id":"https://openalex.org/keywords/structure-based-drug-design","display_name":"structure-based drug design","score":0.7419999837875366}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9836000204086304},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5860999822616577},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5789999961853027},{"id":"https://openalex.org/C192071366","wikidata":"https://www.wikidata.org/wiki/Q2991682","display_name":"Drug design","level":2,"score":0.47380000352859497},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.43479999899864197},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4300000071525574},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4221999943256378},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4056999981403351},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.39910000562667847},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.38589999079704285},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.37229999899864197},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.3644999861717224},{"id":"https://openalex.org/C53105671","wikidata":"https://www.wikidata.org/wiki/Q14777816","display_name":"Rational design","level":2,"score":0.3490999937057495},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.34709998965263367},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.34139999747276306},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32030001282691956},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.3181999921798706},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3089999854564667},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.3001999855041504},{"id":"https://openalex.org/C3019007443","wikidata":"https://www.wikidata.org/wiki/Q568742","display_name":"3d model","level":2,"score":0.27059999108314514},{"id":"https://openalex.org/C3019038264","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug candidate","level":3,"score":0.2667999863624573},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.2635999917984009},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2533000111579895}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.6c01046","doi":"https://doi.org/10.1021/acs.jcim.6c01046","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01046","pdf_url":"https://pubs.acs.org/jcisd8/article-pdf/doi/10.1021/acs.jcim.6c01046/68986526/acs.jcim.6c01046.pdf","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2505.10545","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2505.10545","pdf_url":"https://arxiv.org/pdf/2505.10545","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2505.10545","doi":"https://doi.org/10.48550/arxiv.2505.10545","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2505.10545","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.6c01046","doi":"https://doi.org/10.1021/acs.jcim.6c01046","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01046","pdf_url":"https://pubs.acs.org/jcisd8/article-pdf/doi/10.1021/acs.jcim.6c01046/68986526/acs.jcim.6c01046.pdf","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415201053.pdf","grobid_xml":"https://content.openalex.org/works/W4415201053.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1608885177","https://openalex.org/W1971570097","https://openalex.org/W1971652848","https://openalex.org/W1985588649","https://openalex.org/W1988037271","https://openalex.org/W1992041755","https://openalex.org/W1992905076","https://openalex.org/W2009423060","https://openalex.org/W2045671967","https://openalex.org/W2096541451","https://openalex.org/W2096729078","https://openalex.org/W2106383417","https://openalex.org/W2129069237","https://openalex.org/W2134967712","https://openalex.org/W2153228625","https://openalex.org/W2160592148","https://openalex.org/W2176516200","https://openalex.org/W2177317049","https://openalex.org/W2403144305","https://openalex.org/W2620998958","https://openalex.org/W2754706417","https://openalex.org/W2774836366","https://openalex.org/W2898658380","https://openalex.org/W2902263717","https://openalex.org/W2914635984","https://openalex.org/W2971690404","https://openalex.org/W3034806393","https://openalex.org/W3094123159","https://openalex.org/W3101155908","https://openalex.org/W3159177617","https://openalex.org/W3209790821","https://openalex.org/W4224311800","https://openalex.org/W4306353169","https://openalex.org/W4386804497","https://openalex.org/W4386845335","https://openalex.org/W4387401786","https://openalex.org/W4388464545","https://openalex.org/W4389696354","https://openalex.org/W4392015344","https://openalex.org/W4393222489","https://openalex.org/W4394718179","https://openalex.org/W4396721167","https://openalex.org/W4400410081","https://openalex.org/W4401748232","https://openalex.org/W4402887448","https://openalex.org/W4404051067","https://openalex.org/W4405194591","https://openalex.org/W4408184658","https://openalex.org/W4408293149","https://openalex.org/W4410552772","https://openalex.org/W4411463597","https://openalex.org/W4413705878","https://openalex.org/W4414857975"],"related_works":["https://openalex.org/W7212014820","https://openalex.org/W7164048539","https://openalex.org/W4411348087","https://openalex.org/W4414068485","https://openalex.org/W4404035653","https://openalex.org/W3209790821","https://openalex.org/W7168161375","https://openalex.org/W4413705878","https://openalex.org/W4387401786","https://openalex.org/W4410568075"],"abstract_inverted_index":{"Abstract":[0],"Developing":[1],"bioactive":[2],"molecules":[3],"remains":[4],"a":[5,38,47,57,112,137],"central,":[6],"time-":[7],"and":[8,139],"cost-heavy":[9],"challenge":[10],"in":[11,94,116],"drug":[12,102,118,144],"discovery,":[13],"particularly":[14],"for":[15,28,34,51,123,142],"novel":[16],"targets":[17],"lacking":[18],"structural":[19],"or":[20],"functional":[21],"data.":[22],"Pharmacophore":[23],"modeling":[24,130],"presents":[25],"an":[26,62],"alternative":[27],"capturing":[29],"the":[30,66,70,74,121],"key":[31],"features":[32],"required":[33],"molecular":[35,53,79],"bioactivity":[36],"against":[37],"biological":[39],"target.":[40],"In":[41],"this":[42],"work,":[43],"we":[44],"present":[45],"PharmaDiff,":[46],"pharmacophore-conditioned":[48],"diffusion":[49],"model":[50],"3D":[52,67,78,96,132],"generation.":[54],"PharmaDiff":[55,90,135],"employs":[56],"transformer-based":[58],"architecture":[59],"to":[60,100],"integrate":[61],"atom-based":[63],"representation":[64],"of":[65,77,114],"pharmacophore":[68,85,97,129],"into":[69],"generative":[71,133],"process,":[72],"enabling":[73],"precise":[75],"generation":[76],"graphs":[80],"that":[81],"align":[82],"with":[83,131],"predefined":[84],"hypotheses.":[86],"Through":[87],"comprehensive":[88],"testing,":[89],"demonstrates":[91],"superior":[92],"performance":[93],"matching":[95],"constraints":[98],"compared":[99],"ligand-based":[101],"design":[103],"methods.":[104],"Additionally,":[105],"it":[106],"achieves":[107],"higher":[108],"docking":[109],"scores":[110],"across":[111],"range":[113],"proteins":[115],"structure-based":[117],"design,":[119],"without":[120],"need":[122],"target":[124],"protein":[125],"structures.":[126],"By":[127],"integrating":[128],"techniques,":[134],"offers":[136],"powerful":[138],"flexible":[140],"framework":[141],"rational":[143],"design.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2025-10-15T00:00:00"}