{"id":"https://openalex.org/W7225650983","doi":"https://doi.org/10.1021/acs.jmedchem.6c02199","title":"Autonomous Drug Design via Workflow Agents: Integrating Chemical Semantics and Tool-Oriented Automation","display_name":"Autonomous Drug Design via Workflow Agents: Integrating Chemical Semantics and Tool-Oriented Automation","publication_year":2026,"publication_date":"2026-11-09","ids":{"openalex":"https://openalex.org/W7225650983","doi":"https://doi.org/10.1021/acs.jmedchem.6c02199"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jmedchem.6c02199","doi":"https://doi.org/10.1021/acs.jmedchem.6c02199","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jmedchem.6c02199","pdf_url":null,"source":{"id":"https://openalex.org/S162030435","display_name":"Journal of Medicinal Chemistry","issn_l":"0022-2623","issn":["0022-2623","1520-4804"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-3","ki-jl-2","medline","norway-2","poland-200","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Medicinal Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"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/A5114163404","display_name":"Jingxuan Ge","orcid":"https://orcid.org/0009-0006-9835-5660","observed_orcids":["https://orcid.org/0009-0006-9835-5660"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingxuan Ge","raw_affiliation_strings":["CarbonSilicon AI Technology Company, Ltd. , , ,","Jinhua Institute of Zhejiang University , , , ,","Zhejiang University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CarbonSilicon AI Technology Company, Ltd. , , ,","institution_ids":[]},{"raw_affiliation_string":"Jinhua Institute of Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160043041","display_name":"Youqiao Qian","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Youqiao Qian","raw_affiliation_strings":["Jinhua Institute of Zhejiang University , , , ,","Zhejiang University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jinhua Institute of Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161343243","display_name":"Hao Luo","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hao Luo","raw_affiliation_strings":["CarbonSilicon AI Technology Company, Ltd. , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CarbonSilicon AI Technology Company, Ltd. , , ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008663435","display_name":"Chang\u2010Yu Hsieh","orcid":"https://orcid.org/0000-0002-6242-4218","observed_orcids":["https://orcid.org/0000-0002-6242-4218"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chang-Yu Hsieh","raw_affiliation_strings":["Zhejiang University , , , ,"],"raw_orcid":"https://orcid.org/0000-0002-6242-4218","affiliations":[{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080228020","display_name":"Hui Shi","orcid":"https://orcid.org/0000-0002-4324-414X","observed_orcids":["https://orcid.org/0000-0002-4324-414X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hui Shi","raw_affiliation_strings":["CarbonSilicon AI Technology Company, Ltd. , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CarbonSilicon AI Technology Company, Ltd. , , ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010230212","display_name":"Jian Wu","orcid":"https://orcid.org/0000-0002-8031-9462","observed_orcids":["https://orcid.org/0000-0002-8031-9462"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wu","raw_affiliation_strings":["Zhejiang University , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072525278","display_name":"Peichen Pan","orcid":"https://orcid.org/0000-0003-1152-7759","observed_orcids":["https://orcid.org/0000-0003-1152-7759"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peichen Pan","raw_affiliation_strings":["Zhejiang University , , , ,"],"raw_orcid":"https://orcid.org/0000-0003-1152-7759","affiliations":[{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100624617","display_name":"Yu Kang","orcid":"https://orcid.org/0000-0002-0999-8802","observed_orcids":["https://orcid.org/0000-0002-0999-8802","https://orcid.org/0000-0002-8706-3252"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu Kang","raw_affiliation_strings":["Jinhua Institute of Zhejiang University , , , ,","Zhejiang University , , , ,"],"raw_orcid":"https://orcid.org/0000-0002-0999-8802","affiliations":[{"raw_affiliation_string":"Jinhua Institute of Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028525523","display_name":"Tingjun Hou","orcid":"https://orcid.org/0000-0001-7227-2580","observed_orcids":["https://orcid.org/0000-0001-7227-2580","https://orcid.org/0000-0002-9661-0553"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tingjun Hou","raw_affiliation_strings":["Jinhua Institute of Zhejiang University , , , ,","Zhejiang University , , , ,"],"raw_orcid":"https://orcid.org/0000-0001-7227-2580","affiliations":[{"raw_affiliation_string":"Jinhua Institute of Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Zhejiang University , , , ,","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028525523","https://openalex.org/A5100624617"],"corresponding_institution_ids":["https://openalex.org/I76130692"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"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":0.9994999766349792,"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":0.9994999766349792,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.00019999999494757503,"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/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"}}],"keywords":[{"id":"https://openalex.org/keywords/llm-based-agents","display_name":"LLM agents","score":0.7609999775886536},{"id":"https://openalex.org/keywords/react-framework","display_name":"ReAct framework","score":0.5},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"virtual screening","score":0.5839999914169312},{"id":"https://openalex.org/keywords/de-novo-molecule-generation","display_name":"de novo molecule generation","score":0.9940000176429749},{"id":"https://openalex.org/keywords/molecular-optimization","display_name":"molecular optimization","score":0.925000011920929},{"id":"https://openalex.org/keywords/multi-target-drug-design","display_name":"multi-target drug design","score":0.949999988079071},{"id":"https://openalex.org/keywords/alk-inhibitors","display_name":"ALK inhibitors","score":0.7540000081062317},{"id":"https://openalex.org/keywords/ros1-inhibitors","display_name":"ROS1 inhibitors","score":0.9940000176429749},{"id":"https://openalex.org/keywords/igf1r-inhibitors","display_name":"IGF1R inhibitors","score":0.9950000047683716},{"id":"https://openalex.org/keywords/multi-objective-trade-offs","display_name":"multi-objective trade-offs","score":0.6349999904632568},{"id":"https://openalex.org/keywords/binding-affinity-prediction","display_name":"binding affinity prediction","score":0.49000000953674316},{"id":"https://openalex.org/keywords/toxicity-assessment","display_name":"toxicity prediction","score":0.6140000224113464}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8281000256538391},{"id":"https://openalex.org/C2776303644","wikidata":"https://www.wikidata.org/wiki/Q1020499","display_name":"Interfacing","level":2,"score":0.7391999959945679},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6547999978065491},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5026000142097473},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.49399998784065247},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4860000014305115},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.47620001435279846},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.45660001039505005},{"id":"https://openalex.org/C2780791683","wikidata":"https://www.wikidata.org/wiki/Q846785","display_name":"Action (physics)","level":2,"score":0.4327000081539154},{"id":"https://openalex.org/C13687954","wikidata":"https://www.wikidata.org/wiki/Q4826847","display_name":"Autonomous agent","level":2,"score":0.3806999921798706},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3666999936103821},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.35839998722076416},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3547999858856201},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.3154999911785126},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3003999888896942},{"id":"https://openalex.org/C19612761","wikidata":"https://www.wikidata.org/wiki/Q8034836","display_name":"Workflow technology","level":3,"score":0.28349998593330383},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2741999924182892},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.27070000767707825},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.2583000063896179},{"id":"https://openalex.org/C188220564","wikidata":"https://www.wikidata.org/wiki/Q3325097","display_name":"Workflow engine","level":3,"score":0.257999986410141}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1021/acs.jmedchem.6c02199","doi":"https://doi.org/10.1021/acs.jmedchem.6c02199","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jmedchem.6c02199","pdf_url":null,"source":{"id":"https://openalex.org/S162030435","display_name":"Journal of Medicinal Chemistry","issn_l":"0022-2623","issn":["0022-2623","1520-4804"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-3","ki-jl-2","medline","norway-2","poland-200","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Medicinal Chemistry","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1990626198","https://openalex.org/W1998848097","https://openalex.org/W2052546787","https://openalex.org/W2066417528","https://openalex.org/W2125426232","https://openalex.org/W2163508726","https://openalex.org/W2578240541","https://openalex.org/W3101089668","https://openalex.org/W4289518623","https://openalex.org/W4372330430","https://openalex.org/W4385572408","https://openalex.org/W4386498912","https://openalex.org/W4386976834","https://openalex.org/W4389761608","https://openalex.org/W4389963497","https://openalex.org/W4393936599","https://openalex.org/W4396723768","https://openalex.org/W4396813784","https://openalex.org/W4397004462","https://openalex.org/W4400042185","https://openalex.org/W4401090344","https://openalex.org/W4402170913","https://openalex.org/W4403610674","https://openalex.org/W4404527592","https://openalex.org/W4405185373","https://openalex.org/W4405599065","https://openalex.org/W4406794696","https://openalex.org/W4407789339","https://openalex.org/W4408221130","https://openalex.org/W4409956822","https://openalex.org/W4410325586","https://openalex.org/W4411731716","https://openalex.org/W4412692453","https://openalex.org/W4413000874","https://openalex.org/W4416982455","https://openalex.org/W7127563067","https://openalex.org/W7133209886","https://openalex.org/W7133214447","https://openalex.org/W7133224213","https://openalex.org/W7138193395","https://openalex.org/W7143351253","https://openalex.org/W7147016149","https://openalex.org/W7167845123"],"related_works":["https://openalex.org/W4414587311","https://openalex.org/W6892045942","https://openalex.org/W7221830295","https://openalex.org/W6891941323","https://openalex.org/W7225231441","https://openalex.org/W4416375773","https://openalex.org/W7151056748","https://openalex.org/W7133953733","https://openalex.org/W4414298914","https://openalex.org/W7140173398"],"abstract_inverted_index":{"Abstract":[0],"Large":[1],"language":[2],"model":[3],"(LLM)-based":[4],"agents":[5],"have":[6],"shown":[7],"promise":[8],"in":[9],"automating":[10],"scientific":[11],"tasks,":[12],"yet":[13],"existing":[14],"systems":[15],"for":[16],"drug":[17,38,132],"discovery":[18],"often":[19],"lack":[20],"strategic,":[21],"cross-step":[22,93],"planning,":[23,94],"and":[24,50,55,86,95,107,115],"multi-objective":[25,96],"coordination.":[26],"Here,":[27],"we":[28],"present":[29],"drugflow-skills,":[30],"an":[31],"LLM-driven":[32],"agent":[33,59,89],"framework":[34],"that":[35],"abstracts":[36],"key":[37],"design":[39],"operations,":[40],"including":[41],"virtual":[42],"screening,":[43],"de":[44],"novo":[45],"molecule":[46],"generation,":[47],"molecular":[48],"optimization,":[49],"multi-target":[51],"design,":[52],"into":[53],"composable":[54],"reusable":[56],"skills.":[57],"The":[58],"operates":[60],"under":[61],"a":[62,123],"ReAct":[63],"paradigm,":[64],"executing":[65],"iterative":[66],"\u201cThought":[67],"\u2192":[68,70],"Action":[69],"Observation\u201d":[71],"loops":[72],"while":[73,103],"interfacing":[74],"with":[75],"the":[76,88],"DrugFlow":[77],"backend.":[78],"Across":[79],"five":[80],"representative":[81],"tasks":[82],"targeting":[83],"ALK,":[84],"ROS1,":[85],"IGF-1R,":[87],"demonstrates":[90],"autonomous":[91],"decision-making,":[92],"trade-offs,":[97],"achieving":[98],"improved":[99],"predicted":[100,105],"binding":[101],"scores":[102],"reducing":[104],"toxicity":[106],"off-target":[108],"liabilities.":[109],"It":[110],"also":[111],"provides":[112],"interpretable":[113],"rationales":[114],"adapts":[116],"strategies":[117],"based":[118],"on":[119],"human":[120],"feedback,":[121],"enabling":[122],"human-agent":[124],"co-optimization":[125],"loop.":[126],"These":[127],"results":[128],"support":[129],"dynamic":[130],"reasoning-driven":[131],"design.":[133]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}