{"id":"https://openalex.org/W4377111779","doi":"https://doi.org/10.48550/arxiv.2305.10133","title":"Generation of 3D Molecules in Pockets via Language Model","display_name":"Generation of 3D Molecules in Pockets via Language Model","publication_year":2023,"publication_date":"2023-05-17","ids":{"openalex":"https://openalex.org/W4377111779","doi":"https://doi.org/10.48550/arxiv.2305.10133"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2305.10133","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.10133","pdf_url":"https://arxiv.org/pdf/2305.10133","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2305.10133","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060334150","display_name":"Lvwei Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Feng, Wei","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025545438","display_name":"Zaiyun Lin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Lvwei","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007003792","display_name":"Yanhao Zhu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lin, Zaiyun","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009017466","display_name":"Rong Bai","orcid":"https://orcid.org/0000-0002-3106-7318"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhu, Yanhao","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021320552","display_name":"Wei Feng","orcid":"https://orcid.org/0000-0001-5147-2145"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Han","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063080599","display_name":"Huting Wang","orcid":"https://orcid.org/0009-0008-3956-271X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dong, Jianqiang","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101452132","display_name":"Feng Long","orcid":"https://orcid.org/0009-0008-0065-9119"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bai, Rong","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019479187","display_name":"Wei Peng","orcid":"https://orcid.org/0000-0002-2892-5764"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Huting","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100705731","display_name":"Bo Huang","orcid":"https://orcid.org/0000-0002-5063-3522"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Jielong","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100524959","display_name":"Wenbiao Zhou","orcid":"https://orcid.org/0000-0001-8277-2765"},"institutions":[{"id":"https://openalex.org/I4210138309","display_name":"Center for Innovation","ror":"https://ror.org/04c1v2b17","country_code":"US","type":"facility","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089489","https://openalex.org/I4210138309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng, Wei","raw_affiliation_strings":["Innovation Center for Pathogen Research Guangzhou Laboratory"],"affiliations":[{"raw_affiliation_string":"Innovation Center for Pathogen Research Guangzhou Laboratory","institution_ids":["https://openalex.org/I4210138309"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Huang, Bo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Bo","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]},{"author_position":"last","author":{"id":null,"display_name":"Zhou, Wenbiao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Wenbiao","raw_affiliation_strings":["Beijing StoneWise Technology Co Ltd"],"affiliations":[{"raw_affiliation_string":"Beijing StoneWise Technology Co Ltd","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5060334150"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"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":0.9997000098228455,"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":0.9997000098228455,"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":0.9986000061035156,"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":0.9854000210762024,"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/computer-science","display_name":"Computer science","score":0.7029187679290771},{"id":"https://openalex.org/keywords/notation","display_name":"Notation","score":0.6808573007583618},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5689613223075867},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5596012473106384},{"id":"https://openalex.org/keywords/traverse","display_name":"Traverse","score":0.5515803098678589},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.4965878129005432},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4521215558052063},{"id":"https://openalex.org/keywords/directory","display_name":"Directory","score":0.4495870769023895},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4486697316169739},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4271087348461151},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09867185354232788},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.08125334978103638}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7029187679290771},{"id":"https://openalex.org/C45357846","wikidata":"https://www.wikidata.org/wiki/Q2001982","display_name":"Notation","level":2,"score":0.6808573007583618},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5689613223075867},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5596012473106384},{"id":"https://openalex.org/C176809094","wikidata":"https://www.wikidata.org/wiki/Q15401496","display_name":"Traverse","level":2,"score":0.5515803098678589},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.4965878129005432},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4521215558052063},{"id":"https://openalex.org/C2777683733","wikidata":"https://www.wikidata.org/wiki/Q201456","display_name":"Directory","level":2,"score":0.4495870769023895},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4486697316169739},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4271087348461151},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09867185354232788},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.08125334978103638},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2305.10133","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.10133","pdf_url":"https://arxiv.org/pdf/2305.10133","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"doi:10.48550/arxiv.2305.10133","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2305.10133","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2305.10133","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.10133","pdf_url":"https://arxiv.org/pdf/2305.10133","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.6399999856948853}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W4387506531","https://openalex.org/W4238433571","https://openalex.org/W3174044702","https://openalex.org/W2967848559","https://openalex.org/W4299831724","https://openalex.org/W4283803360"],"abstract_inverted_index":{"Generative":[0],"models":[1,57],"for":[2,102,128],"molecules":[3],"based":[4],"on":[5],"sequential":[6],"line":[7],"notation":[8],"(e.g.":[9],"SMILES)":[10],"or":[11],"graph":[12],"representation":[13],"have":[14],"attracted":[15],"an":[16],"increasing":[17],"interest":[18],"in":[19,80,134],"the":[20,78,103,114],"field":[21],"of":[22,116,121,136],"structure-based":[23],"drug":[24],"design,":[25],"but":[26],"they":[27],"struggle":[28],"to":[29,76,96],"capture":[30],"important":[31],"3D":[32,50],"spatial":[33,86],"interactions":[34],"and":[35,58,71,84,143],"often":[36],"produce":[37],"undesirable":[38],"molecular":[39,65,82],"structures.":[40,118],"To":[41],"address":[42],"these":[43],"challenges,":[44],"we":[45,89],"introduce":[46],"Lingo3DMol,":[47],"a":[48,91],"pocket-based":[49],"molecule":[51,144],"generation":[52,145],"method":[53],"that":[54],"combines":[55],"language":[56],"geometric":[59],"deep":[60],"learning":[61,81],"technology.":[62],"A":[63],"new":[64],"representation,":[66],"fragment-based":[67],"SMILES":[68],"with":[69],"local":[70],"global":[72],"coordinates,":[73],"was":[74,126],"developed":[75],"assist":[77],"model":[79],"topologies":[83],"atomic":[85],"positions.":[87],"Additionally,":[88],"trained":[90],"separate":[92],"noncovalent":[93],"interaction":[94],"predictor":[95],"provide":[97],"essential":[98],"binding":[99,141],"pattern":[100],"information":[101],"generative":[104],"model.":[105],"Lingo3DMol":[106,130],"can":[107],"efficiently":[108],"traverse":[109],"drug-like":[110],"chemical":[111],"spaces,":[112],"preventing":[113],"formation":[115],"unusual":[117],"The":[119],"Directory":[120],"Useful":[122],"Decoys-Enhanced":[123],"(DUD-E)":[124],"dataset":[125],"used":[127],"evaluation.":[129],"outperformed":[131],"state-of-the-art":[132],"methods":[133],"terms":[135],"drug-likeness,":[137],"synthetic":[138],"accessibility,":[139],"pocket":[140],"mode,":[142],"speed.":[146]},"counts_by_year":[],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2023-05-20T00:00:00"}
