{"id":"https://openalex.org/W4403102042","doi":"https://doi.org/10.1021/acs.jcim.4c00683","title":"Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds","display_name":"Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds","publication_year":2024,"publication_date":"2024-10-03","ids":{"openalex":"https://openalex.org/W4403102042","doi":"https://doi.org/10.1021/acs.jcim.4c00683","pmid":"https://pubmed.ncbi.nlm.nih.gov/39360680"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00683","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00683","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.4c00683","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114153331","display_name":"Brendan W. Hall","orcid":"https://orcid.org/0000-0003-1616-1303"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brendan W. Hall","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States","Program in Biophysics, University of California, San Francisco, San Francisco, California 94158, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Program in Biophysics, University of California, San Francisco, San Francisco, California 94158, United States","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001435363","display_name":"Michael J. Keiser","orcid":"https://orcid.org/0000-0002-1240-2192"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210111938","display_name":"Institute for Neurodegenerative Disorders","ror":"https://ror.org/022hrs427","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael J. Keiser","raw_affiliation_strings":["Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California 94158, United States","Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States","Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States","Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California 94158, United States"],"raw_orcid":"https://orcid.org/0000-0002-1240-2192","affiliations":[{"raw_affiliation_string":"Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California 94158, United States","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California 94158, United States","institution_ids":["https://openalex.org/I4210111938","https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5001435363"],"corresponding_institution_ids":["https://openalex.org/I180670191","https://openalex.org/I4210111938"],"apc_list":null,"apc_paid":null,"fwci":1.9138,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.87105165,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"64","issue":"19","first_page":"7398","last_page":"7408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11106","display_name":"Data Management and Algorithms","score":0.9896000027656555,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T11106","display_name":"Data Management and Algorithms","score":0.9896000027656555,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T12288","display_name":"Optimization and Search Problems","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T12292","display_name":"Graph Theory and Algorithms","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/computer-science","display_name":"Computer science","score":0.5979788899421692},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5160043239593506},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4388967454433441},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33801931142807007}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5979788899421692},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5160043239593506},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4388967454433441},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33801931142807007},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"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":"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":"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":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.4c00683","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00683","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39360680","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39360680","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:escholarship.org:ark:/13030/qt43g9s59q","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/43g9s59q","pdf_url":"https://escholarship.org/content/qt43g9s59q/qt43g9s59q.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 64, iss 19","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11480973","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11480973","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11480973/pdf/ci4c00683.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c00683","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00683","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2154969259","display_name":"Decoding the systems pharmacology of proteinopathy in human cells","funder_award_id":"DAF2018-191905","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"}],"funders":[{"id":"https://openalex.org/F4320306192","display_name":"Silicon Valley Community Foundation","ror":"https://ror.org/001ader08"},{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1605923270","https://openalex.org/W1977909079","https://openalex.org/W1984994707","https://openalex.org/W1985588649","https://openalex.org/W1988037271","https://openalex.org/W1988909822","https://openalex.org/W2000350990","https://openalex.org/W2001565801","https://openalex.org/W2009423060","https://openalex.org/W2017254234","https://openalex.org/W2034549041","https://openalex.org/W2040135138","https://openalex.org/W2043014029","https://openalex.org/W2044542784","https://openalex.org/W2058835307","https://openalex.org/W2060531713","https://openalex.org/W2070789802","https://openalex.org/W2076419401","https://openalex.org/W2096729078","https://openalex.org/W2148512505","https://openalex.org/W2164088236","https://openalex.org/W2200017991","https://openalex.org/W2259891323","https://openalex.org/W2608559058","https://openalex.org/W2794994220","https://openalex.org/W2894566366","https://openalex.org/W2912171584","https://openalex.org/W2913668833","https://openalex.org/W2963469388","https://openalex.org/W2963729354","https://openalex.org/W3009970748","https://openalex.org/W3010016408","https://openalex.org/W3014154196","https://openalex.org/W3027975282","https://openalex.org/W3030285818","https://openalex.org/W3112474878","https://openalex.org/W3116865743","https://openalex.org/W3126031592","https://openalex.org/W3135642867","https://openalex.org/W3159598019","https://openalex.org/W3195415198","https://openalex.org/W4200233821","https://openalex.org/W4223920159","https://openalex.org/W4290075791","https://openalex.org/W4316507591","https://openalex.org/W4320857994","https://openalex.org/W4361217414","https://openalex.org/W4379967278","https://openalex.org/W4381839382","https://openalex.org/W4386346641","https://openalex.org/W4392092167","https://openalex.org/W4400242773"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032","https://openalex.org/W2382290278"],"abstract_inverted_index":{"Make-on-demand":[0],"chemical":[1,50,159],"libraries":[2,25],"have":[3],"drastically":[4],"increased":[5],"the":[6,12,30,76,127,155],"reach":[7],"of":[8,37,75,115,126,148,154],"molecular":[9],"docking,":[10],"with":[11,52],"enumerated":[13],"ready-to-dock":[14],"ZINC-22":[15,38],"library":[16,156],"approaching":[17],"6.4":[18],"billion":[19],"molecules":[20],"(July":[21],"2024).":[22],"While":[23],"ever-growing":[24],"result":[26],"in":[27],"better-scoring":[28],"molecules,":[29,110],"computational":[31,88],"resources":[32],"required":[33],"to":[34],"dock":[35],"all":[36],"make":[39],"this":[40],"endeavor":[41],"infeasible":[42],"for":[43,119],"most.":[44],"Here,":[45],"we":[46,59,92],"organize":[47],"and":[48,102,107],"traverse":[49],"space":[51],"hierarchical":[53],"navigable":[54],"small-world":[55],"graphs,":[56],"a":[57,73],"method":[58],"term":[60],"retrieval":[61],"augmented":[62],"docking":[63,71,84,98,152],"(RAD).":[64],"RAD":[65,79,94,112,131,145],"recovers":[66,113,146],"most":[67],"virtual":[68,117,149],"actives,":[69],"despite":[70],"only":[72,124],"fraction":[74],"library.":[77],"Furthermore,":[78],"is":[80],"protein-agnostic,":[81],"supporting":[82],"additional":[83,87],"campaigns":[85,99],"without":[86,157],"overhead.":[89],"In":[90,129],"depth,":[91],"assess":[93],"on":[95],"published":[96],"large-scale":[97],"against":[100,135],"D4":[101],"AmpC":[103],"spanning":[104],"99.5":[105],"million":[106,109,141],"138":[108],"respectively.":[111],"95%":[114],"DOCK":[116],"actives":[118,150],"both":[120],"targets":[121],"after":[122],"evaluating":[123,139],"10%":[125,153],"libraries.":[128],"breadth,":[130],"shows":[132],"widespread":[133],"applicability":[134],"43":[136],"DUDE-Z":[137],"proteins,":[138],"50.3":[140],"associations.":[142],"On":[143],"average,":[144],"87%":[147],"while":[151],"sacrificing":[158],"diversity.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4}],"updated_date":"2026-05-13T08:25:38.343686","created_date":"2025-10-10T00:00:00"}
