{"id":"https://openalex.org/W4409362560","doi":"https://doi.org/10.1609/aaai.v39i24.34804","title":"BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning","display_name":"BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning","publication_year":2025,"publication_date":"2025-04-11","ids":{"openalex":"https://openalex.org/W4409362560","doi":"https://doi.org/10.1609/aaai.v39i24.34804"},"language":"en","primary_location":{"id":"doi:10.1609/aaai.v39i24.34804","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v39i24.34804","pdf_url":"https://ojs.aaai.org/index.php/AAAI/article/download/34804/36959","source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://ojs.aaai.org/index.php/AAAI/article/download/34804/36959","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032713067","display_name":"Artem Zholus","orcid":"https://orcid.org/0000-0003-3167-3585"},"institutions":[{"id":"https://openalex.org/I45683168","display_name":"Polytechnique Montr\u00e9al","ror":"https://ror.org/05f8d4e86","country_code":"CA","type":"education","lineage":["https://openalex.org/I45683168"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Artem Zholus","raw_affiliation_strings":["Insilico Medicine Canada Inc.\nMila \u2013 Quebec AI Institute\n\u00c9cole Polytechnique de Montr\u00e9al\nChandar Research Lab"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insilico Medicine Canada Inc.\nMila \u2013 Quebec AI Institute\n\u00c9cole Polytechnique de Montr\u00e9al\nChandar Research Lab","institution_ids":["https://openalex.org/I45683168"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055576670","display_name":"Maksim Kuznetsov","orcid":"https://orcid.org/0000-0001-8446-7983"},"institutions":[{"id":"https://openalex.org/I4210118119","display_name":"Insilicos (United States)","ror":"https://ror.org/02p5qdz58","country_code":"US","type":"company","lineage":["https://openalex.org/I4210118119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maksim Kuznetsov","raw_affiliation_strings":["Insilico Medicine Canada Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insilico Medicine Canada Inc","institution_ids":["https://openalex.org/I4210118119"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082301279","display_name":"Roman Schutski","orcid":"https://orcid.org/0000-0003-1654-3336"},"institutions":[{"id":"https://openalex.org/I4401200273","display_name":"Insilico Medicine (United States)","ror":"https://ror.org/01mz2wq83","country_code":null,"type":"company","lineage":["https://openalex.org/I4401200273"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Roman Schutski","raw_affiliation_strings":["Insilico Medicine AI Limited"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insilico Medicine AI Limited","institution_ids":["https://openalex.org/I4401200273"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077492338","display_name":"Rim Shayakhmetov","orcid":"https://orcid.org/0000-0001-5425-9964"},"institutions":[{"id":"https://openalex.org/I4210118119","display_name":"Insilicos (United States)","ror":"https://ror.org/02p5qdz58","country_code":"US","type":"company","lineage":["https://openalex.org/I4210118119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rim Shayakhmetov","raw_affiliation_strings":["Insilico Medicine Canada Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insilico Medicine Canada Inc","institution_ids":["https://openalex.org/I4210118119"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061298160","display_name":"Daniil Polykovskiy","orcid":"https://orcid.org/0000-0002-0899-8368"},"institutions":[{"id":"https://openalex.org/I4210118119","display_name":"Insilicos (United States)","ror":"https://ror.org/02p5qdz58","country_code":"US","type":"company","lineage":["https://openalex.org/I4210118119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniil Polykovskiy","raw_affiliation_strings":["Insilico Medicine Canada Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insilico Medicine Canada Inc","institution_ids":["https://openalex.org/I4210118119"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027720969","display_name":"Sarath Chandar","orcid":null},"institutions":[{"id":"https://openalex.org/I45683168","display_name":"Polytechnique Montr\u00e9al","ror":"https://ror.org/05f8d4e86","country_code":"CA","type":"education","lineage":["https://openalex.org/I45683168"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sarath Chandar","raw_affiliation_strings":["Mila \u2013 Quebec AI Institute\n\u00c9cole Polytechnique de Montr\u00e9al\nChandar Research Lab\nCIFAR AI Chair"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mila \u2013 Quebec AI Institute\n\u00c9cole Polytechnique de Montr\u00e9al\nChandar Research Lab\nCIFAR AI Chair","institution_ids":["https://openalex.org/I45683168"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036742375","display_name":"Alex Zhavoronkov","orcid":"https://orcid.org/0000-0001-7067-8966"},"institutions":[{"id":"https://openalex.org/I4401200273","display_name":"Insilico Medicine (United States)","ror":"https://ror.org/01mz2wq83","country_code":null,"type":"company","lineage":["https://openalex.org/I4401200273"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Alex Zhavoronkov","raw_affiliation_strings":["Insilico Medicine AI Limited"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insilico Medicine AI Limited","institution_ids":["https://openalex.org/I4401200273"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":61.9437,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.99969031,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"39","issue":"24","first_page":"26083","last_page":"26091"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9520999789237976,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9520999789237976,"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/T12784","display_name":"Modular Robots and Swarm Intelligence","score":0.9345999956130981,"subfield":{"id":"https://openalex.org/subfields/2210","display_name":"Mechanical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9258000254631042,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/reinforcement-learning","display_name":"Reinforcement learning","score":0.6734041571617126},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6589028835296631},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5223670601844788},{"id":"https://openalex.org/keywords/reinforcement","display_name":"Reinforcement","score":0.5172967910766602},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.4194280207157135},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.39234593510627747},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3370055556297302},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27316462993621826},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.18970322608947754},{"id":"https://openalex.org/keywords/social-psychology","display_name":"Social psychology","score":0.06022772192955017}],"concepts":[{"id":"https://openalex.org/C97541855","wikidata":"https://www.wikidata.org/wiki/Q830687","display_name":"Reinforcement learning","level":2,"score":0.6734041571617126},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6589028835296631},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5223670601844788},{"id":"https://openalex.org/C67203356","wikidata":"https://www.wikidata.org/wiki/Q1321905","display_name":"Reinforcement","level":2,"score":0.5172967910766602},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.4194280207157135},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.39234593510627747},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3370055556297302},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27316462993621826},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.18970322608947754},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.06022772192955017},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1609/aaai.v39i24.34804","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v39i24.34804","pdf_url":"https://ojs.aaai.org/index.php/AAAI/article/download/34804/36959","source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},{"id":"pmh:oai:publications.polymtl.ca:64483","is_oa":false,"landing_page_url":"https://publications.polymtl.ca/64483/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401013","display_name":"PolyPublie (\u00c9cole Polytechnique de Montr\u00e9al)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45683168","host_organization_name":"Polytechnique Montr\u00e9al","host_organization_lineage":["https://openalex.org/I45683168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article de revue"},{"id":"pmh:oai:ojs.aaai.org:article/34804","is_oa":false,"landing_page_url":"https://ojs.aaai.org/index.php/AAAI/article/view/34804","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2159-5399","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1609/aaai.v39i24.34804","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v39i24.34804","pdf_url":"https://ojs.aaai.org/index.php/AAAI/article/download/34804/36959","source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309949","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409362560.pdf","grobid_xml":"https://content.openalex.org/works/W4409362560.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4310083477","https://openalex.org/W2328553770","https://openalex.org/W2920061524","https://openalex.org/W1977959518","https://openalex.org/W2038908348","https://openalex.org/W2107890255","https://openalex.org/W2106552856","https://openalex.org/W2145821588","https://openalex.org/W2086122291","https://openalex.org/W1987513656"],"abstract_inverted_index":{"Generating":[0],"novel":[1,35],"active":[2],"molecules":[3,50],"for":[4,13,67],"a":[5,34,41,77,95,107,112,121,145],"given":[6],"protein":[7],"is":[8],"an":[9,18,68],"extremely":[10],"challenging":[11],"task":[12],"generative":[14,36,110],"models":[15],"that":[16],"requires":[17],"understanding":[19],"of":[20,139,176],"the":[21,26,52,65,103,117,127,137,161],"complex":[22],"physical":[23],"interactions":[24],"between":[25],"molecule":[27,124],"and":[28,61,80,120,152,168],"its":[29],"environment.":[30],"This":[31],"paper":[32],"presents":[33],"model,":[37,111],"BindGPT,":[38],"which":[39],"uses":[40],"conceptually":[42],"simple":[43,146],"but":[44],"powerful":[45],"approach":[46,148],"to":[47,179],"create":[48],"3D":[49,108,123],"within":[51],"protein's":[53],"binding":[54],"site.":[55],"Our":[56],"model":[57,99,128],"produces":[58],"molecular":[59,109,118],"graphs":[60],"conformations":[62],"jointly,":[63],"eliminating":[64],"need":[66],"extra":[69],"graph":[70,169],"reconstruction":[71],"step.":[72],"We":[73,92,141],"pre-train":[74],"BindGPT":[75],"on":[76,116,156],"large-scale":[78],"dataset":[79],"fine-tune":[81],"it":[82],"with":[83,150],"reinforcement":[84],"learning":[85],"using":[86],"scores":[87],"from":[88],"external":[89],"simulation":[90],"software.":[91],"demonstrate":[93],"how":[94,143],"single":[96],"pre-trained":[97],"language":[98,166],"can":[100,154],"serve":[101],"at":[102],"same":[104],"time":[105],"as":[106],"conformer":[113],"generator":[114],"conditioned":[115],"graph,":[119],"pocket-conditioned":[122],"generator.":[125],"Notably,":[126],"does":[129],"not":[130],"make":[131],"any":[132],"representational":[133],"equivariance":[134],"assumptions":[135],"about":[136],"domain":[138],"generation.":[140],"show":[142],"such":[144],"conceptual":[147],"combined":[149],"pre-training":[151],"scaling":[153],"perform":[155],"par":[157],"or":[158],"better":[159],"than":[160],"current":[162],"best-specialized":[163],"diffusion":[164],"models,":[165,167],"neural":[170],"networks":[171],"while":[172],"being":[173],"two":[174],"orders":[175],"magnitude":[177],"cheaper":[178],"sample.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":5}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}
