{"id":"https://openalex.org/W4280562526","doi":"https://doi.org/10.1021/acs.jcim.2c00042","title":"Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models","display_name":"Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models","publication_year":2022,"publication_date":"2022-05-11","ids":{"openalex":"https://openalex.org/W4280562526","doi":"https://doi.org/10.1021/acs.jcim.2c00042","pmid":"https://pubmed.ncbi.nlm.nih.gov/35544331"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00042","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00042","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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108515305","display_name":"Weixin Xie","orcid":"https://orcid.org/0000-0002-7747-0348"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weixin Xie","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074854163","display_name":"Fanhao Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fanhao Wang","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100357549","display_name":"Yibo Li","orcid":"https://orcid.org/0000-0002-4174-8600"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yibo Li","raw_affiliation_strings":["Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210160507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064049271","display_name":"Luhua Lai","orcid":"https://orcid.org/0000-0002-8343-7587"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Luhua Lai","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","Peking-Tsinghua Center for Life Science at BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China"],"raw_orcid":"https://orcid.org/0000-0002-8343-7587","affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Peking-Tsinghua Center for Life Science at BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210116048","https://openalex.org/I4210160507"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047704083","display_name":"Jianfeng Pei","orcid":"https://orcid.org/0000-0002-8482-1185"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianfeng Pei","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":"https://orcid.org/0000-0002-8482-1185","affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047704083"],"corresponding_institution_ids":["https://openalex.org/I20231570"],"apc_list":null,"apc_paid":null,"fwci":8.6187,"has_fulltext":false,"cited_by_count":75,"citation_normalized_percentile":{"value":0.98382808,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"62","issue":"10","first_page":"2269","last_page":"2279"},"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":0.9847999811172485,"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":0.9648000001907349,"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/generative-grammar","display_name":"Generative grammar","score":0.7953755855560303},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6486789584159851},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.56560218334198},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5181304812431335},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5153431296348572},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4988589286804199},{"id":"https://openalex.org/keywords/generative-design","display_name":"Generative Design","score":0.43854427337646484},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37479138374328613},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3662286400794983},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.15901437401771545},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.15188834071159363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11060896515846252}],"concepts":[{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.7953755855560303},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6486789584159851},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.56560218334198},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5181304812431335},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5153431296348572},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4988589286804199},{"id":"https://openalex.org/C184408114","wikidata":"https://www.wikidata.org/wiki/Q1502022","display_name":"Generative Design","level":3,"score":0.43854427337646484},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37479138374328613},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3662286400794983},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15901437401771545},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.15188834071159363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11060896515846252},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.0}],"mesh":[{"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00042","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00042","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35544331","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35544331","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","score":0.46000000834465027,"display_name":"Decent work and economic growth"}],"awards":[{"id":"https://openalex.org/G1108311842","display_name":null,"funder_award_id":"22033001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2815554813","display_name":null,"funder_award_id":"21673010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7057204618","display_name":null,"funder_award_id":"2018ZX09711002","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1968319881","https://openalex.org/W1975147762","https://openalex.org/W1980969309","https://openalex.org/W2011230643","https://openalex.org/W2028629022","https://openalex.org/W2077467665","https://openalex.org/W2147421370","https://openalex.org/W2169678694","https://openalex.org/W2396663079","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2583907533","https://openalex.org/W2610148085","https://openalex.org/W2617750324","https://openalex.org/W2765224015","https://openalex.org/W2835515562","https://openalex.org/W2891365537","https://openalex.org/W2900694120","https://openalex.org/W2912212024","https://openalex.org/W2912328818","https://openalex.org/W2914635984","https://openalex.org/W2915175970","https://openalex.org/W2969980075","https://openalex.org/W2971690404","https://openalex.org/W2984249386","https://openalex.org/W2994178060","https://openalex.org/W3007133919","https://openalex.org/W3011847211","https://openalex.org/W3014154196","https://openalex.org/W3027975282","https://openalex.org/W3042210295","https://openalex.org/W3043096321","https://openalex.org/W3094686696","https://openalex.org/W3116727726","https://openalex.org/W3116865743","https://openalex.org/W3119872582","https://openalex.org/W3121082297","https://openalex.org/W3174777205","https://openalex.org/W3200806939","https://openalex.org/W3205590463","https://openalex.org/W3209416355","https://openalex.org/W3209764902","https://openalex.org/W3209790821","https://openalex.org/W4287148389"],"related_works":["https://openalex.org/W4301024388","https://openalex.org/W775311126","https://openalex.org/W4300030714","https://openalex.org/W4391334978","https://openalex.org/W1517876498","https://openalex.org/W2489288131","https://openalex.org/W4317695495","https://openalex.org/W4380551139","https://openalex.org/W4388137171","https://openalex.org/W1967909251"],"abstract_inverted_index":{"A":[0],"persistent":[1],"goal":[2],"for":[3,71,104],"de":[4,105],"novo":[5,106],"drug":[6,107],"design":[7,79],"is":[8],"to":[9,30,51,77],"generate":[10,52],"novel":[11],"chemical":[12],"compounds":[13],"with":[14,97],"desirable":[15],"properties":[16],"in":[17,42,82,91],"a":[18,83],"labor-,":[19],"time-,":[20],"and":[21,36,75,100],"cost-efficient":[22],"manner.":[23,85],"Deep":[24],"generative":[25,57,94],"models":[26,58,95],"provide":[27],"alternative":[28],"routes":[29],"this":[31],"goal.":[32],"Numerous":[33],"model":[34],"architectures":[35],"optimization":[37],"strategies":[38],"have":[39,48,65],"been":[40,49,67],"explored":[41],"recent":[43],"years,":[44],"most":[45],"of":[46],"which":[47],"developed":[50],"two-dimensional":[53],"molecular":[54,93],"structures.":[55],"Some":[56],"aiming":[59],"at":[60],"three-dimensional":[61],"(3D)":[62],"molecule":[63],"generation":[64],"also":[66],"proposed,":[68],"gaining":[69],"attention":[70],"their":[72],"unique":[73],"advantages":[74],"potential":[76],"directly":[78],"drug-like":[80],"molecules":[81],"target-conditioning":[84],"This":[86],"review":[87],"highlights":[88],"current":[89],"developments":[90],"3D":[92],"combined":[96],"deep":[98],"learning":[99],"discusses":[101],"future":[102],"directions":[103],"design.":[108]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":31},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":8}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
