{"id":"https://openalex.org/W2911569513","doi":"https://doi.org/10.1021/acs.jcim.9b00195","title":"A Quantum-Inspired Method for Three-Dimensional Ligand-Based Virtual Screening","display_name":"A Quantum-Inspired Method for Three-Dimensional Ligand-Based Virtual Screening","publication_year":2019,"publication_date":"2019-10-18","ids":{"openalex":"https://openalex.org/W2911569513","doi":"https://doi.org/10.1021/acs.jcim.9b00195","mag":"2911569513","pmid":"https://pubmed.ncbi.nlm.nih.gov/31625746"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00195","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00195","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":"article","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1902.00352","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Maritza Hernandez","orcid":"https://orcid.org/0000-0003-1869-8243"},"institutions":[{"id":"https://openalex.org/I4210143237","display_name":"QLT (Canada)","ror":"https://ror.org/03qqc4d32","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210143237"]},{"id":"https://openalex.org/I4387154962","display_name":"1QBit","ror":"https://ror.org/04eswfz98","country_code":null,"type":"company","lineage":["https://openalex.org/I4387154962"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Maritza Hernandez","raw_affiliation_strings":["1QB Information Technologies (1QBit), 200-1285 West Pender Street, Vancouver, BC V6E 4B1, Canada"],"raw_orcid":"https://orcid.org/0000-0003-1869-8243","affiliations":[{"raw_affiliation_string":"1QB Information Technologies (1QBit), 200-1285 West Pender Street, Vancouver, BC V6E 4B1, Canada","institution_ids":["https://openalex.org/I4210143237","https://openalex.org/I4387154962"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Guo Liang Gan","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210143237","display_name":"QLT (Canada)","ror":"https://ror.org/03qqc4d32","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210143237"]},{"id":"https://openalex.org/I4387154962","display_name":"1QBit","ror":"https://ror.org/04eswfz98","country_code":null,"type":"company","lineage":["https://openalex.org/I4387154962"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Guo Liang Gan","raw_affiliation_strings":["1QB Information Technologies (1QBit), 200-1285 West Pender Street, Vancouver, BC V6E 4B1, Canada","School of Computing Science, Simon Fraser University, 8888 University Drive, Vancouver, BC V5A 1S6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1QB Information Technologies (1QBit), 200-1285 West Pender Street, Vancouver, BC V6E 4B1, Canada","institution_ids":["https://openalex.org/I4210143237","https://openalex.org/I4387154962"]},{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, 8888 University Drive, Vancouver, BC V5A 1S6, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Kirby Linvill","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099672","display_name":"Accenture (United States)","ror":"https://ror.org/013g16z83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210093804","https://openalex.org/I4210099672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirby Linvill","raw_affiliation_strings":["Accenture Labs, Accenture PLC, 415 Mission Street, Suite 3300, San Francisco, California 94105, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accenture Labs, Accenture PLC, 415 Mission Street, Suite 3300, San Francisco, California 94105, United States","institution_ids":["https://openalex.org/I4210099672"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Carl Dukatz","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099672","display_name":"Accenture (United States)","ror":"https://ror.org/013g16z83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210093804","https://openalex.org/I4210099672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carl Dukatz","raw_affiliation_strings":["Accenture Labs, Accenture PLC, 415 Mission Street, Suite 3300, San Francisco, California 94105, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accenture Labs, Accenture PLC, 415 Mission Street, Suite 3300, San Francisco, California 94105, United States","institution_ids":["https://openalex.org/I4210099672"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jun Feng","orcid":null},"institutions":[{"id":"https://openalex.org/I1297540436","display_name":"Biogen (United States)","ror":"https://ror.org/02jqkb192","country_code":"US","type":"company","lineage":["https://openalex.org/I1297540436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Feng","raw_affiliation_strings":["Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I1297540436"]}]},{"author_position":"last","author":{"id":null,"display_name":"Govinda Bhisetti","orcid":null},"institutions":[{"id":"https://openalex.org/I1297540436","display_name":"Biogen (United States)","ror":"https://ror.org/02jqkb192","country_code":"US","type":"company","lineage":["https://openalex.org/I1297540436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Govinda Bhisetti","raw_affiliation_strings":["Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I1297540436"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210143237","https://openalex.org/I4387154962"],"apc_list":null,"apc_paid":null,"fwci":1.5412,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.84052919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"59","issue":"10","first_page":"4475","last_page":"4485"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9919000267982483,"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":0.9919000267982483,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0010000000474974513,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.0008999999845400453,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/fingerprint","display_name":"Fingerprint (computing)","score":0.754800021648407},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.6897000074386597},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.661899983882904},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.5733000040054321},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5701000094413757},{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.5278000235557556}],"concepts":[{"id":"https://openalex.org/C2777826928","wikidata":"https://www.wikidata.org/wiki/Q3745713","display_name":"Fingerprint (computing)","level":2,"score":0.754800021648407},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.696399986743927},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.6897000074386597},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.661899983882904},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.5733000040054321},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5701000094413757},{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.5278000235557556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5227000117301941},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43209999799728394},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3750999867916107},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.32359999418258667},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3181000053882599},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.2833999991416931},{"id":"https://openalex.org/C168406668","wikidata":"https://www.wikidata.org/wiki/Q178022","display_name":"Fingerprint recognition","level":3,"score":0.2824999988079071},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2752000093460083},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.27480000257492065},{"id":"https://openalex.org/C129844170","wikidata":"https://www.wikidata.org/wiki/Q41299","display_name":"Quadratic equation","level":2,"score":0.2630999982357025}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b00195","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00195","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:31625746","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31625746","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:1902.00352","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1902.00352","pdf_url":"https://arxiv.org/pdf/1902.00352","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":null,"raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1902.00352","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1902.00352","pdf_url":"https://arxiv.org/pdf/1902.00352","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":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1595350250","https://openalex.org/W1968319881","https://openalex.org/W1970208561","https://openalex.org/W1975664878","https://openalex.org/W1988037271","https://openalex.org/W1990451437","https://openalex.org/W1999491936","https://openalex.org/W2001816314","https://openalex.org/W2008732224","https://openalex.org/W2014123957","https://openalex.org/W2024610405","https://openalex.org/W2024860775","https://openalex.org/W2025135899","https://openalex.org/W2027065525","https://openalex.org/W2030735938","https://openalex.org/W2058820833","https://openalex.org/W2067837249","https://openalex.org/W2075186867","https://openalex.org/W2081322171","https://openalex.org/W2103626206","https://openalex.org/W2105614108","https://openalex.org/W2125109129","https://openalex.org/W2127760066","https://openalex.org/W2130479394","https://openalex.org/W2169088933","https://openalex.org/W2169546341","https://openalex.org/W2172024214","https://openalex.org/W2177317049","https://openalex.org/W2253909748","https://openalex.org/W2290847742","https://openalex.org/W2318547308","https://openalex.org/W2412446857","https://openalex.org/W2576148114","https://openalex.org/W2791137739"],"related_works":[],"abstract_inverted_index":{"Measuring":[0],"similarity":[1,28,39,66],"between":[2],"molecules":[3,30],"is":[4,75],"an":[5],"important":[6],"part":[7],"of":[8,18,29,54,98,165,185],"virtual":[9],"screening":[10],"(VS)":[11],"experiments":[12],"deployed":[13],"during":[14],"the":[15,27,51,93,128,139,163,166,177,186,196],"early":[16,156],"stages":[17],"drug":[19],"discovery.":[20],"Most":[21],"widely":[22],"used":[23],"methods":[24,40,182],"for":[25,69,152,183,198],"evaluating":[26],"use":[31],"molecular":[32,55,65],"fingerprints":[33],"to":[34,95,113],"encode":[35],"structural":[36],"information.":[37],"While":[38],"using":[41,88,146],"fingerprint":[42,171,181],"encodings":[43],"are":[44],"efficient,":[45],"they":[46],"do":[47],"not":[48],"consider":[49,109],"all":[50],"relevant":[52,112],"aspects":[53],"structure.":[56],"In":[57,105,159],"this":[58,99,106,133],"paper,":[59],"we":[60,108,161],"describe":[61],"a":[62,78,89,189],"quantum-inspired":[63],"graph-based":[64],"(GMS)":[67],"method":[68,74,168,179],"ligand-based":[70,114,193],"VS.":[71],"The":[72,173],"GMS":[73,129,167,178],"formulated":[76],"as":[77,117,150],"quadratic":[79],"unconstrained":[80],"binary":[81],"optimization":[82],"problem":[83],"that":[84,145,176],"can":[85],"be":[86],"solved":[87],"quantum":[90],"annealer,":[91],"providing":[92],"opportunity":[94],"take":[96],"advantage":[97],"nascent":[100],"and":[101,120,124],"potentially":[102],"groundbreaking":[103],"technology.":[104],"study,":[107],"various":[110,136],"features":[111,119,151],"VS,":[115],"such":[116],"pharmacophore":[118],"three-dimensional":[121,147],"atomic":[122,148],"coordinates,":[123],"include":[125],"them":[126],"in":[127,192],"method.":[130],"We":[131],"evaluate":[132,162],"approach":[134],"on":[135],"datasets":[137],"from":[138],"DUD_LIB_VS_1.0":[140],"library.":[141],"Our":[142],"results":[143,174],"show":[144],"coordinates":[149],"comparison":[153],"yields":[154],"higher":[155],"enrichment":[157],"values.":[158],"addition,":[160],"performance":[164],"against":[169],"conventional":[170],"approaches.":[172],"demonstrate":[175],"outperforms":[180],"most":[184],"datasets,":[187],"presenting":[188],"new":[190],"alternative":[191],"VS":[194],"with":[195],"potential":[197],"future":[199],"enhancement.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2019-02-21T00:00:00"}
