{"id":"https://openalex.org/W4412695666","doi":"https://doi.org/10.1021/acs.jcim.5c01020","title":"Benchmarking 3D Structure-Based Molecule Generators","display_name":"Benchmarking 3D Structure-Based Molecule Generators","publication_year":2025,"publication_date":"2025-07-25","ids":{"openalex":"https://openalex.org/W4412695666","doi":"https://doi.org/10.1021/acs.jcim.5c01020","pmid":"https://pubmed.ncbi.nlm.nih.gov/40711830"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01020","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01020","pdf_url":null,"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,"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"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.5c01020","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116831683","display_name":"Natasha Sanjrani","orcid":null},"institutions":[{"id":"https://openalex.org/I181647926","display_name":"University of Strathclyde","ror":"https://ror.org/00n3w3b69","country_code":"GB","type":"education","lineage":["https://openalex.org/I181647926"]},{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Natasha Sanjrani","raw_affiliation_strings":["Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K","Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K"],"affiliations":[{"raw_affiliation_string":"Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K","institution_ids":["https://openalex.org/I2800110054"]},{"raw_affiliation_string":"Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K","institution_ids":["https://openalex.org/I181647926"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063127789","display_name":"Damien Coupry","orcid":"https://orcid.org/0000-0001-6053-2381"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Damien E. Coupry","raw_affiliation_strings":["Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K"],"affiliations":[{"raw_affiliation_string":"Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K","institution_ids":["https://openalex.org/I2800110054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032112911","display_name":"P\u00e9ter Pog\u00e1ny","orcid":"https://orcid.org/0000-0003-3536-0746"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Pog\u00e1ny","raw_affiliation_strings":["Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K"],"affiliations":[{"raw_affiliation_string":"Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K","institution_ids":["https://openalex.org/I2800110054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069304320","display_name":"David Scott Palmer","orcid":"https://orcid.org/0000-0003-4356-9144"},"institutions":[{"id":"https://openalex.org/I181647926","display_name":"University of Strathclyde","ror":"https://ror.org/00n3w3b69","country_code":"GB","type":"education","lineage":["https://openalex.org/I181647926"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David S. Palmer","raw_affiliation_strings":["Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K"],"affiliations":[{"raw_affiliation_string":"Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K","institution_ids":["https://openalex.org/I181647926"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079075074","display_name":"Stephen D. Pickett","orcid":"https://orcid.org/0000-0002-0958-9830"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stephen D. Pickett","raw_affiliation_strings":["Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K"],"affiliations":[{"raw_affiliation_string":"Department of Cheminformatics, Research Technologies, GSK, Gunnels Wood Road, Stevenage SG1 2NY, U.K","institution_ids":["https://openalex.org/I2800110054"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5116831683"],"corresponding_institution_ids":["https://openalex.org/I181647926","https://openalex.org/I2800110054"],"apc_list":null,"apc_paid":null,"fwci":4.3639,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.94714647,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"65","issue":"15","first_page":"8006","last_page":"8021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991999864578247,"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":0.9991999864578247,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9934999942779541,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/benchmarking","display_name":"Benchmarking","score":0.7908966541290283},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6943202614784241},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6578980088233948},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6481171250343323},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5676576495170593},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.47278356552124023},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46567294001579285},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.41146716475486755},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.23094519972801208},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06260812282562256}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7908966541290283},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6943202614784241},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6578980088233948},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6481171250343323},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5676576495170593},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47278356552124023},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46567294001579285},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.41146716475486755},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.23094519972801208},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06260812282562256},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D015195","descriptor_name":"Drug Design","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058990","descriptor_name":"Molecular Targeted Therapy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058990","descriptor_name":"Molecular Targeted Therapy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058990","descriptor_name":"Molecular Targeted Therapy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.5c01020","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01020","pdf_url":null,"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,"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":"pmid:40711830","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40711830","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:strathprints.strath.ac.uk:93571","is_oa":true,"landing_page_url":"https://strathprints.strath.ac.uk/view/author/1559530.html>","pdf_url":"https://strathprints.strath.ac.uk/93571/19/Sanjrani-etal-JCIM-2025-Benchmarking-3D-structure-based-molecule-generators.pdf","source":{"id":"https://openalex.org/S4306402226","display_name":"Strathprints: The University of Strathclyde institutional repository (University of Strathclyde)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I181647926","host_organization_name":"University of Strathclyde","host_organization_lineage":["https://openalex.org/I181647926"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:europepmc.org:11155703","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12344697","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"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c01020","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01020","pdf_url":null,"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,"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320307773","display_name":"GlaxoSmithKline","ror":"https://ror.org/01xsqw823"},{"id":"https://openalex.org/F4320310234","display_name":"University of Strathclyde","ror":"https://ror.org/00n3w3b69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W1968319881","https://openalex.org/W1980969309","https://openalex.org/W2017254234","https://openalex.org/W2021848632","https://openalex.org/W2026724025","https://openalex.org/W2028279608","https://openalex.org/W2041686943","https://openalex.org/W2092285329","https://openalex.org/W2094568831","https://openalex.org/W2096541451","https://openalex.org/W2121895929","https://openalex.org/W2170088433","https://openalex.org/W2319902168","https://openalex.org/W2346710580","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2594183968","https://openalex.org/W2618625858","https://openalex.org/W2620998958","https://openalex.org/W2786565076","https://openalex.org/W2786722833","https://openalex.org/W2793945656","https://openalex.org/W2799435340","https://openalex.org/W2805002767","https://openalex.org/W2805516822","https://openalex.org/W2835515562","https://openalex.org/W2900694120","https://openalex.org/W2945551948","https://openalex.org/W2953128081","https://openalex.org/W2991736596","https://openalex.org/W3007133919","https://openalex.org/W3015572666","https://openalex.org/W3024423177","https://openalex.org/W3025593963","https://openalex.org/W3082411326","https://openalex.org/W3094640617","https://openalex.org/W3098269892","https://openalex.org/W3116865743","https://openalex.org/W3121082297","https://openalex.org/W3126031592","https://openalex.org/W3127347132","https://openalex.org/W3133989558","https://openalex.org/W3138474425","https://openalex.org/W3157286395","https://openalex.org/W3159177617","https://openalex.org/W3177828909","https://openalex.org/W3181995918","https://openalex.org/W3200806939","https://openalex.org/W3208515103","https://openalex.org/W3209764902","https://openalex.org/W3214740101","https://openalex.org/W4200382722","https://openalex.org/W4221138292","https://openalex.org/W4221155201","https://openalex.org/W4224311800","https://openalex.org/W4224865292","https://openalex.org/W4252520800","https://openalex.org/W4280535976","https://openalex.org/W4280562526","https://openalex.org/W4281381643","https://openalex.org/W4281619372","https://openalex.org/W4283075725","https://openalex.org/W4285179478","https://openalex.org/W4287556187","https://openalex.org/W4287589317","https://openalex.org/W4289436753","https://openalex.org/W4297434538","https://openalex.org/W4297951436","https://openalex.org/W4318912574","https://openalex.org/W4319758801","https://openalex.org/W4321276167","https://openalex.org/W4321455550","https://openalex.org/W4323650483","https://openalex.org/W4361198756","https://openalex.org/W4376632842","https://openalex.org/W4378071155","https://openalex.org/W4385407166","https://openalex.org/W4385889851","https://openalex.org/W4386316087","https://openalex.org/W4387294353","https://openalex.org/W4387882024","https://openalex.org/W4388520183","https://openalex.org/W4388567308","https://openalex.org/W4389696354","https://openalex.org/W4391940739","https://openalex.org/W4392653998","https://openalex.org/W4393100383","https://openalex.org/W4393181728","https://openalex.org/W4393222489","https://openalex.org/W4394718179","https://openalex.org/W4399669868","https://openalex.org/W4400435053","https://openalex.org/W4400795417","https://openalex.org/W4404997118","https://openalex.org/W4405194591","https://openalex.org/W4405437765","https://openalex.org/W4405592636","https://openalex.org/W4409566068"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W4399363378","https://openalex.org/W4380075502"],"abstract_inverted_index":{"To":[0],"understand":[1,132],"the":[2,20,31,40,133],"benefits":[3],"and":[4,9,26,47,52,54,59,76,84,118,138],"drawbacks":[5],"of":[6,22,120,135],"3D":[7,27,77,115],"combinatorial":[8,55,80,137],"deep":[10,67,104,139],"learning":[11,68,105,140],"generators,":[12,45],"a":[13,36],"novel":[14],"benchmark":[15,127],"was":[16,64],"created":[17],"focusing":[18],"on":[19,112],"recreation":[21,119],"important":[23,121],"protein-ligand":[24],"interactions":[25],"ligand":[28,116],"conformations.":[29],"Using":[30],"BindingMOAD":[32],"data":[33],"set":[34],"with":[35],"hold-out":[37],"blind":[38],"set,":[39],"sequential":[41],"graph":[42],"neural":[43],"network":[44],"Pocket2Mol":[46],"PocketFlow,":[48],"diffusion":[49],"models,":[50],"DiffSBDD":[51],"MolSnapper,":[53],"genetic":[56],"algorithms,":[57],"AutoGrow4":[58],"LigBuilderV3,":[60],"were":[61],"evaluated.":[62],"It":[63],"discovered":[65],"that":[66,87],"methods":[69,81],"fail":[70],"to":[71,90,131],"generate":[72,85],"structurally":[73],"valid":[74],"molecules":[75,86],"conformations,":[78,117],"whereas":[79],"are":[82,88],"slow":[83],"prone":[89],"failing":[91],"2D":[92],"MOSES":[93],"filters.":[94],"The":[95,142],"results":[96],"from":[97],"this":[98],"evaluation":[99],"guide":[100],"us":[101],"toward":[102],"improving":[103],"structure-based":[106],"generators":[107],"by":[108],"placing":[109],"higher":[110],"importance":[111],"structural":[113],"validity,":[114],"known":[122],"active":[123],"site":[124],"interactions.":[125],"This":[126],"should":[128],"be":[129],"used":[130],"limitations":[134],"future":[136],"generators.":[141],"package":[143],"is":[144],"freely":[145],"available":[146],"under":[147],"an":[148],"Apache":[149],"2.0":[150],"license":[151],"at":[152],"github.com/gskcheminformatics/SBDD-benchmarking.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
