{"id":"https://openalex.org/W4321377212","doi":"https://doi.org/10.1186/s13321-023-00694-z","title":"DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning","display_name":"DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning","publication_year":2023,"publication_date":"2023-02-20","ids":{"openalex":"https://openalex.org/W4321377212","doi":"https://doi.org/10.1186/s13321-023-00694-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/36803659"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00694-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00694-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00694-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00694-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037255059","display_name":"Xuhan Liu","orcid":"https://orcid.org/0000-0003-2368-4655"},"institutions":[{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Xuhan Liu","raw_affiliation_strings":["Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032548139","display_name":"Kai Ye","orcid":"https://orcid.org/0000-0002-2851-6741"},"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":"Kai Ye","raw_affiliation_strings":["School of Electrics and Information Engineering, Xi'an Jiaotong University, 28 XianningW Rd, Xi'an, China"],"affiliations":[{"raw_affiliation_string":"School of Electrics and Information Engineering, Xi'an Jiaotong University, 28 XianningW Rd, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015253529","display_name":"Herman van Vlijmen","orcid":"https://orcid.org/0000-0002-1915-3141"},"institutions":[{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]},{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE","NL"],"is_corresponding":false,"raw_author_name":"Herman W. T. van Vlijmen","raw_affiliation_strings":["Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands","Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium"],"affiliations":[{"raw_affiliation_string":"Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171"]},{"raw_affiliation_string":"Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065525958","display_name":"Adriaan P. IJzerman","orcid":"https://orcid.org/0000-0002-1182-2259"},"institutions":[{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Adriaan P. IJzerman","raw_affiliation_strings":["Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088996741","display_name":"Gerard J. P. van Westen","orcid":"https://orcid.org/0000-0003-0717-1817"},"institutions":[{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Gerard J. P. van Westen","raw_affiliation_strings":["Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands. gerard@lacdr.leidenuniv.nl","Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands. gerard@lacdr.leidenuniv.nl","institution_ids":["https://openalex.org/I4210133171"]},{"raw_affiliation_string":"Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5037255059"],"corresponding_institution_ids":["https://openalex.org/I4210133171"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":15.5332,"has_fulltext":true,"cited_by_count":78,"citation_normalized_percentile":{"value":0.9934621,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"24","last_page":"24"},"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/T11440","display_name":"Click Chemistry and Applications","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.993399977684021,"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/reinforcement-learning","display_name":"Reinforcement learning","score":0.837026059627533},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7659139037132263},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.611026406288147},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.4733583927154541},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.44307440519332886},{"id":"https://openalex.org/keywords/scaffold","display_name":"Scaffold","score":0.4400756061077118},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.4200684130191803},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40053844451904297},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16978180408477783},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10366129875183105},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09666338562965393}],"concepts":[{"id":"https://openalex.org/C97541855","wikidata":"https://www.wikidata.org/wiki/Q830687","display_name":"Reinforcement learning","level":2,"score":0.837026059627533},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7659139037132263},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.611026406288147},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.4733583927154541},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.44307440519332886},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.4400756061077118},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.4200684130191803},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40053844451904297},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16978180408477783},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10366129875183105},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09666338562965393},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-023-00694-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00694-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00694-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},{"id":"pmid:36803659","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36803659","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 cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9940339","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9940339","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9940339/pdf/13321_2023_Article_694.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3590045","is_oa":true,"landing_page_url":"https://hdl.handle.net/1887/3590045","pdf_url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3590046/view","source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"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":"Journal of Cheminformatics","raw_type":"Article / Letter to editor"},{"id":"pmh:oai:doaj.org/article:12e2403ede4e4bc28f5d4d15dd0d5517","is_oa":true,"landing_page_url":"https://doaj.org/article/12e2403ede4e4bc28f5d4d15dd0d5517","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":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-14 (2023)","raw_type":"article"},{"id":"pmh:ul:oai:scholarlypublications.universiteitleiden.nl:item_3590045","is_oa":true,"landing_page_url":"http://hdl.handle.net/1887/3590045","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"Journal of Cheminformatics, 15(1):24","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00694-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00694-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00694-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G2300736770","display_name":null,"funder_award_id":"(CSC)","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G3759882581","display_name":null,"funder_award_id":"14410","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G3858139783","display_name":null,"funder_award_id":"STW-Veni #14410","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4321377212.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W959778778","https://openalex.org/W1500036797","https://openalex.org/W1531916394","https://openalex.org/W1975391500","https://openalex.org/W1979406691","https://openalex.org/W1995530068","https://openalex.org/W2022476850","https://openalex.org/W2023818227","https://openalex.org/W2034549041","https://openalex.org/W2046258407","https://openalex.org/W2050535564","https://openalex.org/W2051947720","https://openalex.org/W2096541451","https://openalex.org/W2122624834","https://openalex.org/W2160592148","https://openalex.org/W2529996553","https://openalex.org/W2558217333","https://openalex.org/W2578240541","https://openalex.org/W2610148085","https://openalex.org/W2740946158","https://openalex.org/W2767357245","https://openalex.org/W2797324131","https://openalex.org/W2919115771","https://openalex.org/W2947161483","https://openalex.org/W2947950688","https://openalex.org/W2992072991","https://openalex.org/W2992613109","https://openalex.org/W3030948478","https://openalex.org/W3044640842","https://openalex.org/W3080671367","https://openalex.org/W3094686696","https://openalex.org/W3098269892","https://openalex.org/W3158535672"],"related_works":["https://openalex.org/W2973074952","https://openalex.org/W1973026729","https://openalex.org/W4283395020","https://openalex.org/W4320732452","https://openalex.org/W135095951","https://openalex.org/W4286980196","https://openalex.org/W4385588199","https://openalex.org/W3199987505","https://openalex.org/W4385760073","https://openalex.org/W2600435468"],"abstract_inverted_index":{"Rational":[0],"drug":[1,38,51,109],"design":[2,108,236],"often":[3],"starts":[4],"from":[5,202],"specific":[6],"scaffolds":[7,113,146],"to":[8,17,24,88,99,107,128,144,152,159,219,235],"which":[9,62,114],"side":[10],"chains/substituents":[11],"are":[12,258],"added":[13],"or":[14],"modified":[15],"due":[16],"the":[18,31,75,101,162,184,187,210,221,231,239,255],"large":[19],"drug-like":[20,28],"chemical":[21],"space":[22],"available":[23],"search":[25],"for":[26,48,171,198,238],"novel":[27,168],"molecules.":[29],"With":[30],"rapid":[32],"growth":[33],"of":[34,42,116,165,186,223,229,254,262],"deep":[35,71,138],"learning":[36,139,217],"in":[37,66],"discovery,":[39],"a":[40,58,94,123,135,150,167,203,215,227,265],"variety":[41],"effective":[43],"approaches":[44],"have":[45],"been":[46],"developed":[47],"de":[49],"novo":[50],"design.":[52],"In":[53,97,157],"previous":[54,76],"work":[55],"we":[56,104],"proposed":[57],"method":[59,232],"named":[60],"DrugEx,":[61],"can":[63],"be":[64],"applied":[65,234],"polypharmacology":[67],"based":[68,111,176,206],"on":[69,112,177,207],"multi-objective":[70],"reinforcement":[72,216],"learning.":[73],"However,":[74],"version":[77],"is":[78,134],"trained":[79,213],"under":[80,214],"fixed":[81],"objectives":[82],"and":[83,149,174,195,244,260],"does":[84],"not":[85],"allow":[86],"users":[87],"input":[89,148],"any":[90],"prior":[91],"information":[92],"(i.e.":[93],"desired":[95,224],"scaffold).":[96],"order":[98,158],"improve":[100],"general":[102],"applicability,":[103],"updated":[105],"DrugEx":[106],"molecules":[110,154,166,257],"consist":[115],"multiple":[117],"fragments":[118],"provided":[119],"by":[120],"users.":[121],"Here,":[122],"Transformer":[124,133,191],"model":[125,140,192],"was":[126,181,212,233],"employed":[127],"generate":[129,153],"molecular":[130],"structures.":[131],"The":[132,189,249],"multi-head":[136],"self-attention":[137],"containing":[141],"an":[142,178],"encoder":[143],"receive":[145],"as":[147,155],"decoder":[151],"output.":[156],"deal":[160],"with":[161,246,272],"graph":[163,190],"representation":[164],"positional":[169],"encoding":[170],"each":[172],"atom":[173],"bond":[175],"adjacency":[179],"matrix":[180],"proposed,":[182],"extending":[183],"architecture":[185],"Transformer.":[188],"contains":[193],"growing":[194],"connecting":[196],"procedures":[197],"molecule":[199],"generation":[200],"starting":[201],"given":[204,273],"scaffold":[205],"fragments.":[208],"Moreover,":[209],"generator":[211],"framework":[218],"increase":[220],"number":[222],"ligands.":[225],"As":[226],"proof":[228],"concept,":[230],"ligands":[237],"adenosine":[240],"A<sub>2A</sub>":[241],"receptor":[242],"(A<sub>2A</sub>AR)":[243],"compared":[245],"SMILES-based":[247],"methods.":[248],"results":[250],"show":[251],"that":[252],"100%":[253],"generated":[256],"valid":[259],"most":[261],"them":[263],"had":[264],"high":[266],"predicted":[267],"affinity":[268],"value":[269],"towards":[270],"A<sub>2A</sub>AR":[271],"scaffolds.":[274]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":29},{"year":2024,"cited_by_count":30},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
