{"id":"https://openalex.org/W2210838452","doi":"https://doi.org/10.1021/ci6003338","title":"QUASI:\u2009 A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity","display_name":"QUASI:\u2009 A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity","publication_year":2007,"publication_date":"2007-05-01","ids":{"openalex":"https://openalex.org/W2210838452","doi":"https://doi.org/10.1021/ci6003338","mag":"2210838452","pmid":"https://pubmed.ncbi.nlm.nih.gov/17497844"},"language":"en","primary_location":{"id":"doi:10.1021/ci6003338","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci6003338","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":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5105420951","display_name":"Nikolay P. Todorov","orcid":null},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Nikolay P. Todorov","raw_affiliation_strings":["De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075915311","display_name":"Ian L. Alberts","orcid":"https://orcid.org/0000-0002-8992-4407"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ian L. Alberts","raw_affiliation_strings":["De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044455499","display_name":"Iwan J. P. de Esch","orcid":"https://orcid.org/0000-0002-1969-0238"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Iwan J. P. de Esch","raw_affiliation_strings":["De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111370890","display_name":"Philip M. Dean","orcid":null},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Philip M. Dean","raw_affiliation_strings":["De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"De Novo Pharmaceuticals Ltd., Vision Park, Histon, Cambridge CB49ZR, U.K., and Department of Pharmacochemistry, Vrije Universiteit, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5105420951"],"corresponding_institution_ids":["https://openalex.org/I865915315"],"apc_list":null,"apc_paid":null,"fwci":4.5141,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.94852345,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"47","issue":"3","first_page":"1007","last_page":"1020"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9925000071525574,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9887999892234802,"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/superposition-principle","display_name":"Superposition principle","score":0.8628365993499756},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.654455304145813},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5570110082626343},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5384158492088318},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5073477625846863},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.48905548453330994},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.44739216566085815},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4430259168148041},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.42361754179000854},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3898332417011261},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.385715126991272},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3466222882270813},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.30907708406448364},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3002798855304718},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.23396092653274536},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1867256760597229},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17962875962257385},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.15767553448677063},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14956402778625488},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.12297624349594116},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0995013415813446}],"concepts":[{"id":"https://openalex.org/C27753989","wikidata":"https://www.wikidata.org/wiki/Q284885","display_name":"Superposition principle","level":2,"score":0.8628365993499756},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.654455304145813},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5570110082626343},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5384158492088318},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5073477625846863},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.48905548453330994},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.44739216566085815},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4430259168148041},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.42361754179000854},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3898332417011261},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.385715126991272},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3466222882270813},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.30907708406448364},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3002798855304718},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.23396092653274536},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1867256760597229},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17962875962257385},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.15767553448677063},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14956402778625488},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.12297624349594116},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0995013415813446},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1021/ci6003338","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci6003338","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:17497844","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17497844","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:vu:oai:research.vu.nl:publications/fc537a79-0a6e-45cb-afc0-9d6d421a2eed","is_oa":false,"landing_page_url":"https://research.vu.nl/en/publications/fc537a79-0a6e-45cb-afc0-9d6d421a2eed","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, 47(3), 1007 - 20. American Chemical Society","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1493926273","https://openalex.org/W1508244629","https://openalex.org/W1575639801","https://openalex.org/W1963679143","https://openalex.org/W1964512781","https://openalex.org/W1971458166","https://openalex.org/W1991591168","https://openalex.org/W1994067196","https://openalex.org/W1995852445","https://openalex.org/W2002380876","https://openalex.org/W2005097199","https://openalex.org/W2007746855","https://openalex.org/W2016369317","https://openalex.org/W2024060531","https://openalex.org/W2040496005","https://openalex.org/W2046311259","https://openalex.org/W2056593372","https://openalex.org/W2067455153","https://openalex.org/W2075016969","https://openalex.org/W2077124804","https://openalex.org/W2082153551","https://openalex.org/W2114779636","https://openalex.org/W2124319366","https://openalex.org/W2136567909","https://openalex.org/W2161117347","https://openalex.org/W2171839634","https://openalex.org/W2320753102","https://openalex.org/W2485932750","https://openalex.org/W2950369396"],"related_works":["https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2336040088","https://openalex.org/W4292296636","https://openalex.org/W4255337529","https://openalex.org/W3042279869","https://openalex.org/W1963790256","https://openalex.org/W2090768198"],"abstract_inverted_index":{"The":[0,101],"structure":[1],"of":[2,26,30,37,42,54,77,136,155],"many":[3],"receptors":[4],"is":[5,16,21,57,86,104,117,123,140],"unknown,":[6],"and":[7,35,65,80,106,130],"only":[8,81],"information":[9],"about":[10],"diverse":[11,144],"ligands":[12,56,71],"binding":[13],"to":[14,47,74,90,142,151,162],"them":[15],"available.":[17],"A":[18],"new":[19],"method":[20],"presented":[22],"for":[23,40],"the":[24,38,52,67,70,78,109,133,137,147],"superposition":[25,116,126,138],"such":[27],"ligands,":[28],"derivation":[29],"putative":[31],"receptor":[32,50,92,102],"site":[33,79,93],"models":[34,39,127,148],"utilization":[36],"screening":[41],"compound":[43],"databases.":[44],"In":[45],"order":[46],"generate":[48],"a":[49,91,97,153],"model,":[51],"similarity":[53,85],"all":[55],"optimized":[58],"simultaneously":[59],"taking":[60],"into":[61],"account":[62],"conformational":[63,121],"flexibility":[64,122],"also":[66],"possibility":[68],"that":[69],"can":[72],"bind":[73],"different":[75,125],"regions":[76],"partially":[82],"overlap.":[83],"Ligand":[84],"defined":[87],"with":[88,108,132],"respect":[89],"model":[94,103],"serving":[95],"as":[96],"common":[98],"reference":[99],"frame.":[100],"dynamic":[105],"coevolves":[107],"ligand":[110,120],"alignment":[111],"until":[112],"an":[113],"optimal":[114],"self-consistent":[115],"achieved.":[118],"When":[119,146],"permitted,":[124],"are":[128,149,159],"possible":[129],"consistent":[131],"data.":[134],"Clustering":[135],"solutions":[139],"used":[141,150],"obtain":[143],"models.":[145],"screen":[152],"database":[154],"compounds,":[156],"high":[157],"enrichments":[158],"obtained,":[160],"comparable":[161],"those":[163],"obtained":[164],"in":[165],"docking":[166],"studies.":[167]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}