{"id":"https://openalex.org/W4404181791","doi":"https://doi.org/10.1038/s43588-024-00718-0","title":"A deep learning approach for rational ligand generation with toxicity control via reactive building blocks","display_name":"A deep learning approach for rational ligand generation with toxicity control via reactive building blocks","publication_year":2024,"publication_date":"2024-11-08","ids":{"openalex":"https://openalex.org/W4404181791","doi":"https://doi.org/10.1038/s43588-024-00718-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/39516375"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-024-00718-0","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-024-00718-0","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","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/A5036428356","display_name":"Pengyong Li","orcid":"https://orcid.org/0000-0001-5971-046X"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengyong Li","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023306071","display_name":"K.N. Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaihao Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China"],"raw_orcid":"https://orcid.org/0009-0001-8405-3905","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046037333","display_name":"Tianxiao Liu","orcid":"https://orcid.org/0000-0001-5050-8804"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianxiao Liu","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064632912","display_name":"Ruiqiang Lu","orcid":"https://orcid.org/0000-0002-5333-9062"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Ruiqiang Lu","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100760185","display_name":"Yangyang Chen","orcid":"https://orcid.org/0000-0002-3521-475X"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yangyang Chen","raw_affiliation_strings":["University of Tsukuba, Tsukuba, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Tsukuba, Tsukuba, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037785133","display_name":"Xiaojun Yao","orcid":"https://orcid.org/0000-0002-8974-0173"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Xiaojun Yao","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083753621","display_name":"Lin Gao","orcid":"https://orcid.org/0000-0002-1781-4671"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Gao","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027286013","display_name":"Xiangxiang Zeng","orcid":"https://orcid.org/0000-0001-6201-0114"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]},{"id":"https://openalex.org/I198357462","display_name":"Changsha University","ror":"https://ror.org/011d8sm39","country_code":"CN","type":"education","lineage":["https://openalex.org/I198357462"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, China. xzeng@hnu.edu.cn","College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"],"raw_orcid":"https://orcid.org/0000-0003-1081-7658","affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China. xzeng@hnu.edu.cn","institution_ids":["https://openalex.org/I198357462","https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5027286013"],"corresponding_institution_ids":["https://openalex.org/I16609230","https://openalex.org/I198357462"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":4.0312,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.94702753,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"4","issue":"11","first_page":"851","last_page":"864"},"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/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":1.0,"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":0.9968000054359436,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9884999990463257,"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/ligand","display_name":"Ligand (biochemistry)","score":0.541617214679718},{"id":"https://openalex.org/keywords/toxicity","display_name":"Toxicity","score":0.49146783351898193},{"id":"https://openalex.org/keywords/rational-design","display_name":"Rational design","score":0.474489688873291},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4726618528366089},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39597511291503906},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3778444230556488},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3738211393356323},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.22347784042358398},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.1715354025363922},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09053030610084534},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07666200399398804}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.541617214679718},{"id":"https://openalex.org/C29730261","wikidata":"https://www.wikidata.org/wiki/Q274160","display_name":"Toxicity","level":2,"score":0.49146783351898193},{"id":"https://openalex.org/C53105671","wikidata":"https://www.wikidata.org/wiki/Q14777816","display_name":"Rational design","level":2,"score":0.474489688873291},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4726618528366089},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39597511291503906},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3778444230556488},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3738211393356323},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.22347784042358398},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.1715354025363922},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09053030610084534},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07666200399398804},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-024-00718-0","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-024-00718-0","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:39516375","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39516375","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":"Nature computational science","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W2017423606","https://openalex.org/W2022476850","https://openalex.org/W2024060531","https://openalex.org/W2034549041","https://openalex.org/W2036043110","https://openalex.org/W2046370400","https://openalex.org/W2056760934","https://openalex.org/W2059412995","https://openalex.org/W2060531713","https://openalex.org/W2066273100","https://openalex.org/W2074978477","https://openalex.org/W2092285329","https://openalex.org/W2108389384","https://openalex.org/W2134967712","https://openalex.org/W2151697120","https://openalex.org/W2160592148","https://openalex.org/W2200017991","https://openalex.org/W2244785476","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2612027503","https://openalex.org/W2805002767","https://openalex.org/W2900090807","https://openalex.org/W2950954328","https://openalex.org/W2955219525","https://openalex.org/W2962717182","https://openalex.org/W2963028280","https://openalex.org/W2963223306","https://openalex.org/W3011286504","https://openalex.org/W3014154196","https://openalex.org/W3036527662","https://openalex.org/W3082411326","https://openalex.org/W3097627562","https://openalex.org/W3099414221","https://openalex.org/W3127521151","https://openalex.org/W3165171933","https://openalex.org/W3168436232","https://openalex.org/W3209764902","https://openalex.org/W3217546525","https://openalex.org/W4230167402","https://openalex.org/W4286500588","https://openalex.org/W4307416138","https://openalex.org/W4309412288","https://openalex.org/W4327550249","https://openalex.org/W4399393786","https://openalex.org/W6688384872","https://openalex.org/W6756224866","https://openalex.org/W6817391364","https://openalex.org/W6893147749"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756","https://openalex.org/W4323565446"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
