{"id":"https://openalex.org/W4414068485","doi":"https://doi.org/10.3389/fbinf.2025.1628800","title":"PharmacoForge: pharmacophore generation with diffusion models","display_name":"PharmacoForge: pharmacophore generation with diffusion models","publication_year":2025,"publication_date":"2025-09-08","ids":{"openalex":"https://openalex.org/W4414068485","doi":"https://doi.org/10.3389/fbinf.2025.1628800","pmid":"https://pubmed.ncbi.nlm.nih.gov/40989749"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1628800","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1628800","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1628800/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1628800/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5117642390","display_name":"Emma Flynn","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"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":"Emma L. Flynn","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Riya Shah","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Riya Shah","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041584278","display_name":"Ian Dunn","orcid":"https://orcid.org/0000-0002-4493-4708"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"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":"Ian Dunn","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088892534","display_name":"Rishal Aggarwal","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"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":"Rishal Aggarwal","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040700924","display_name":"David Ryan Koes","orcid":"https://orcid.org/0000-0002-6892-6614"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Ryan Koes","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5040700924"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.2433245,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1628800","last_page":"1628800"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.984499990940094,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.982699990272522,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.9922999739646912},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.8029000163078308},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5271000266075134},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.46230000257492065},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.40230000019073486},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4000000059604645}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9922999739646912},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8029000163078308},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6022999882698059},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5271000266075134},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.46230000257492065},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.40230000019073486},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4000000059604645},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3815000057220459},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3698999881744385},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.3675999939441681},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36640000343322754},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3569999933242798},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3431999981403351},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.3310999870300293},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3197999894618988},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28859999775886536},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.28110000491142273}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2025.1628800","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1628800","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1628800/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40989749","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40989749","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:2ef0cb307a30487cade6efbd11a14fd6","is_oa":true,"landing_page_url":"https://doaj.org/article/2ef0cb307a30487cade6efbd11a14fd6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11260733","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12451294","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"pmh:oai:pubmedcentral.nih.gov:12451294","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12451294/","pdf_url":null,"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":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1628800","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1628800","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1628800/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414068485.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1500036797","https://openalex.org/W1968319881","https://openalex.org/W1975447903","https://openalex.org/W2016155858","https://openalex.org/W2033016300","https://openalex.org/W2134967712","https://openalex.org/W2217770415","https://openalex.org/W2336883206","https://openalex.org/W2481799911","https://openalex.org/W2948831670","https://openalex.org/W3015572666","https://openalex.org/W3027975282","https://openalex.org/W3036167779","https://openalex.org/W3048377477","https://openalex.org/W3082411326","https://openalex.org/W3168430821","https://openalex.org/W3209764902","https://openalex.org/W3209790821","https://openalex.org/W4206018883","https://openalex.org/W4206912588","https://openalex.org/W4210617107","https://openalex.org/W4281476460","https://openalex.org/W4283075725","https://openalex.org/W4307416138","https://openalex.org/W4311825396","https://openalex.org/W4367049415","https://openalex.org/W4387401786","https://openalex.org/W4388963710","https://openalex.org/W4396813916","https://openalex.org/W4405902512","https://openalex.org/W4405955232","https://openalex.org/W4409566068"],"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":{"Structure-based":[0],"drug":[1],"design":[2],"(SBDD)":[3],"is":[4],"enhanced":[5],"by":[6,30],"machine":[7],"learning":[8],"(ML)":[9],"to":[10,91,149,156,165],"improve":[11],"both":[12,25],"virtual":[13],"screening":[14,27,126],"and":[15,32,41,109,141,159],"<i>de":[16,150,166],"novo</i>":[17,151,167],"design.":[18],"Despite":[19],"advances":[20],"in":[21,57,137],"ML":[22],"tools":[23],"for":[24,74],"strategies,":[26],"remains":[28],"bounded":[29],"time":[31,46],"computational":[33],"cost,":[34],"while":[35],"generative":[36,111],"models":[37,112],"frequently":[38],"produce":[39],"invalid":[40],"synthetically":[42],"inaccessible":[43],"molecules.":[44,96],"Screening":[45],"can":[47],"be":[48,92],"improved":[49],"with":[50],"pharmacophore":[51,63,84,102,121,134,145],"search,":[52],"which":[53],"quickly":[54],"identifies":[55],"ligands":[56,87,143,153],"a":[58,62,71,80,114,124],"database":[59],"that":[60,88],"match":[61],"query.":[64],"In":[65],"this":[66],"work,":[67],"we":[68],"introduce":[69],"PharmacoForge,":[70],"diffusion":[72],"model":[73],"generating":[75],"3D":[76],"pharmacophores":[77],"conditioned":[78],"on":[79],"protein":[81],"pocket.":[82],"Generated":[83],"queries":[85,146],"identify":[86],"are":[89],"guaranteed":[90],"valid,":[93],"commercially":[94],"available":[95],"We":[97,118],"evaluate":[98],"PharmacoForge":[99,131],"against":[100],"automated":[101],"generation":[103,135],"methods":[104,136],"using":[105],"the":[106,128,138],"LIT-PCBA":[107,139],"benchmark":[108],"ligand":[110],"through":[113,123],"docking-based":[115],"evaluation":[116],"framework.":[117],"further":[119],"assess":[120],"quality":[122],"retrospective":[125],"of":[127],"DUD-E":[129,157],"dataset.":[130],"surpasses":[132],"other":[133],"benchmark,":[140],"resulting":[142],"from":[144],"performed":[147],"similarly":[148],"generated":[152,168],"when":[154],"docking":[155],"targets":[158],"had":[160],"lower":[161],"strain":[162],"energies":[163],"compared":[164],"ligands.":[169]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}