{"id":"https://openalex.org/W4392822085","doi":"https://doi.org/10.1021/acs.jcim.3c01816","title":"Physics-Informed Generative Model for Drug-like Molecule Conformers","display_name":"Physics-Informed Generative Model for Drug-like Molecule Conformers","publication_year":2024,"publication_date":"2024-03-15","ids":{"openalex":"https://openalex.org/W4392822085","doi":"https://doi.org/10.1021/acs.jcim.3c01816","pmid":"https://pubmed.ncbi.nlm.nih.gov/38486425"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01816","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01816","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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 Chemical Information and Modeling","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2403.07925","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"David C. Williams","orcid":"https://orcid.org/0000-0002-4123-9339"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"David C. Williams","raw_affiliation_strings":["Nobias Therapeutics, Inc., 144 S Whisman Rd, Suite C, Mountain View, California 94041, United States"],"raw_orcid":"https://orcid.org/0000-0002-4123-9339","affiliations":[{"raw_affiliation_string":"Nobias Therapeutics, Inc., 144 S Whisman Rd, Suite C, Mountain View, California 94041, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5094155741","display_name":"Neil Inala","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Neil Inala","raw_affiliation_strings":["Nobias Therapeutics, Inc., 144 S Whisman Rd, Suite C, Mountain View, California 94041, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nobias Therapeutics, Inc., 144 S Whisman Rd, Suite C, Mountain View, California 94041, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5094155741"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.6993,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.84821932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"64","issue":"8","first_page":"2988","last_page":"3007"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8614000082015991,"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":0.8614000082015991,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.7068613767623901},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.606736958026886},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4713439643383026},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.44309136271476746},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.44216859340667725},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.3284871578216553},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3118305206298828},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23480379581451416},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.230138897895813},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.21634361147880554},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20046010613441467},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.14166733622550964},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.10439276695251465}],"concepts":[{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.7068613767623901},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.606736958026886},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4713439643383026},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.44309136271476746},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.44216859340667725},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.3284871578216553},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3118305206298828},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23480379581451416},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.230138897895813},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.21634361147880554},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20046010613441467},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.14166733622550964},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.10439276695251465}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010825","descriptor_name":"Physics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.3c01816","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01816","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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 Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38486425","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38486425","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:arXiv.org:2403.07925","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2403.07925","pdf_url":"https://arxiv.org/pdf/2403.07925","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-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:figshare.com:article/25415216","is_oa":true,"landing_page_url":null,"pdf_url":"https://figshare.com/articles/journal_contribution/Physics-Informed_Generative_Model_for_Drug-like_Molecule_Conformers/25415216","source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2403.07925","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2403.07925","pdf_url":"https://arxiv.org/pdf/2403.07925","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-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W1963607000","https://openalex.org/W1967689294","https://openalex.org/W1986240377","https://openalex.org/W1994052145","https://openalex.org/W2012684279","https://openalex.org/W2013035813","https://openalex.org/W2014123957","https://openalex.org/W2020040806","https://openalex.org/W2022242214","https://openalex.org/W2035349592","https://openalex.org/W2036570914","https://openalex.org/W2037481719","https://openalex.org/W2052818547","https://openalex.org/W2066273100","https://openalex.org/W2072537419","https://openalex.org/W2074808135","https://openalex.org/W2078374001","https://openalex.org/W2084693609","https://openalex.org/W2088178727","https://openalex.org/W2118233996","https://openalex.org/W2129069237","https://openalex.org/W2147421370","https://openalex.org/W2154777073","https://openalex.org/W2158604280","https://openalex.org/W2170481351","https://openalex.org/W2244785476","https://openalex.org/W2578119541","https://openalex.org/W2594183968","https://openalex.org/W2605801743","https://openalex.org/W2726184500","https://openalex.org/W2761273232","https://openalex.org/W2900090807","https://openalex.org/W2902556395","https://openalex.org/W2908510526","https://openalex.org/W2911997094","https://openalex.org/W2916045588","https://openalex.org/W2931367569","https://openalex.org/W2945976633","https://openalex.org/W2962711740","https://openalex.org/W3011847211","https://openalex.org/W3011894284","https://openalex.org/W3013954280","https://openalex.org/W3034806393","https://openalex.org/W3108554146","https://openalex.org/W3110257065","https://openalex.org/W3119095170","https://openalex.org/W3121370741","https://openalex.org/W3129651364","https://openalex.org/W3180196270","https://openalex.org/W3199173685","https://openalex.org/W3210035614","https://openalex.org/W4221149941","https://openalex.org/W4282053982","https://openalex.org/W4286795917","https://openalex.org/W4288102734","https://openalex.org/W4292754606","https://openalex.org/W4293327156","https://openalex.org/W4302307901","https://openalex.org/W4307468223","https://openalex.org/W4312933868","https://openalex.org/W4323076585","https://openalex.org/W4360884927","https://openalex.org/W4362679702","https://openalex.org/W4388821018","https://openalex.org/W4391769935"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W2280377497","https://openalex.org/W4387506531","https://openalex.org/W4238433571","https://openalex.org/W3174044702","https://openalex.org/W2967848559","https://openalex.org/W4283803360"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,35,53],"diffusion-based":[3,67],"generative":[4],"model":[5,10],"for":[6,90],"conformer":[7],"generation.":[8,68],"Our":[9],"is":[11,21,58,88],"focused":[12],"on":[13,71],"the":[14,17,24,82,107,111],"reproduction":[15],"of":[16,63,76,95],"bonded":[18,91],"structure":[19],"and":[20,49,110],"constructed":[22],"from":[23,52,106],"associated":[25],"terms":[26],"traditionally":[27],"found":[28],"in":[29,40,66],"classical":[30],"force":[31],"fields":[32],"to":[33,45,103],"ensure":[34],"physically":[36],"relevant":[37],"representation.":[38],"Techniques":[39],"deep":[41],"learning":[42],"are":[43,100],"used":[44],"infer":[46],"atom":[47],"typing":[48],"geometric":[50],"parameters":[51],"training":[54,70],"set.":[55],"Conformer":[56],"sampling":[57],"achieved":[59,89],"by":[60],"taking":[61],"advantage":[62],"recent":[64],"advancements":[65],"By":[69],"large,":[72],"synthetic":[73],"data":[74],"sets":[75],"diverse,":[77],"drug-like":[78],"molecules":[79],"optimized":[80],"with":[81],"semiempirical":[83],"GFN2-xTB":[84],"method,":[85],"high":[86],"accuracy":[87],"parameters,":[92],"exceeding":[93],"that":[94],"conventional,":[96],"knowledge-based":[97],"methods.":[98],"Results":[99],"also":[101],"compared":[102],"experimental":[104],"structures":[105],"Protein":[108],"Databank":[109],"Cambridge":[112],"Structural":[113],"Database.":[114]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-10T08:33:47.465468","created_date":"2025-10-10T00:00:00"}