{"id":"https://openalex.org/W3143357176","doi":"https://doi.org/10.1021/acs.jcim.0c01382","title":"Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses","display_name":"Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses","publication_year":2021,"publication_date":"2021-04-02","ids":{"openalex":"https://openalex.org/W3143357176","doi":"https://doi.org/10.1021/acs.jcim.0c01382","mag":"3143357176","pmid":"https://pubmed.ncbi.nlm.nih.gov/33797240","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8154257"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c01382","doi":"https://doi.org/10.1021/acs.jcim.0c01382","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01382","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.0c01382","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068691245","display_name":"Hrvoje Rimac","orcid":"https://orcid.org/0000-0001-7232-6489","observed_orcids":["https://orcid.org/0000-0001-7232-6489"]},"institutions":[{"id":"https://openalex.org/I181343428","display_name":"University of Zagreb","ror":"https://ror.org/00mv6sv71","country_code":"HR","type":"education","lineage":["https://openalex.org/I181343428"]}],"countries":["HR"],"is_corresponding":true,"raw_author_name":"Hrvoje Rimac","raw_affiliation_strings":["Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kova\u010di\u0107a 1, 10000 Zagreb, Croatia"],"raw_orcid":"https://orcid.org/0000-0001-7232-6489","affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kova\u010di\u0107a 1, 10000 Zagreb, Croatia","institution_ids":["https://openalex.org/I181343428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037290428","display_name":"Maria Grishina","orcid":"https://orcid.org/0000-0002-2573-4831","observed_orcids":["https://orcid.org/0000-0002-2573-4831"]},"institutions":[{"id":"https://openalex.org/I107640659","display_name":"South Ural State University","ror":"https://ror.org/03sfk2504","country_code":"RU","type":"education","lineage":["https://openalex.org/I107640659"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Maria Grishina","raw_affiliation_strings":["Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chaikovskogo 20A, Chelyabinsk 454008, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chaikovskogo 20A, Chelyabinsk 454008, Russia","institution_ids":["https://openalex.org/I107640659"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032912231","display_name":"Vladimir Potemkin","orcid":"https://orcid.org/0000-0002-5244-8718","observed_orcids":["https://orcid.org/0000-0002-5244-8718"]},"institutions":[{"id":"https://openalex.org/I107640659","display_name":"South Ural State University","ror":"https://ror.org/03sfk2504","country_code":"RU","type":"education","lineage":["https://openalex.org/I107640659"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vladimir Potemkin","raw_affiliation_strings":["Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chaikovskogo 20A, Chelyabinsk 454008, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chaikovskogo 20A, Chelyabinsk 454008, Russia","institution_ids":["https://openalex.org/I107640659"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037290428","https://openalex.org/A5068691245"],"corresponding_institution_ids":["https://openalex.org/I107640659","https://openalex.org/I181343428"],"apc_list":{"value":5000,"currency":"USD","value_usd":5000},"apc_paid":{"value":5000,"currency":"USD","value_usd":5000},"fwci":1.8434,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.86089434,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"61","issue":"4","first_page":"1801","last_page":"1813"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.6909999847412109},{"id":"https://openalex.org/keywords/principle-of-complementarity","display_name":"complementarity principle","score":0.9100000262260437},{"id":"https://openalex.org/keywords/ligand-receptor-interactions","display_name":"ligand-receptor interactions","score":0.7549999952316284},{"id":"https://openalex.org/keywords/electron-density","display_name":"electron density","score":0.6729999780654907}],"concepts":[{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.7116751670837402},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7050840854644775},{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.6295584440231323},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5718798637390137},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.44042131304740906},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37744903564453125},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34816625714302063},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3427908718585968},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.33876916766166687},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3346903324127197},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.2724623680114746},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23461222648620605},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14250388741493225},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.0c01382","doi":"https://doi.org/10.1021/acs.jcim.0c01382","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01382","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8154257","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8154257/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8154257/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,"listed_in":[],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmid:33797240","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33797240","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,"listed_in":[],"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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.0c01382","doi":"https://doi.org/10.1021/acs.jcim.0c01382","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01382","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G8780475976","display_name":null,"funder_award_id":"20-415-740008","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"}],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3143357176.pdf","grobid_xml":"https://content.openalex.org/works/W3143357176.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1606947757","https://openalex.org/W1653739410","https://openalex.org/W1965525854","https://openalex.org/W1986240377","https://openalex.org/W2024723494","https://openalex.org/W2035540344","https://openalex.org/W2037535298","https://openalex.org/W2063622629","https://openalex.org/W2067455153","https://openalex.org/W2068573355","https://openalex.org/W2105668062","https://openalex.org/W2132629607","https://openalex.org/W2134967712","https://openalex.org/W2152964937","https://openalex.org/W2297560509","https://openalex.org/W2404280981","https://openalex.org/W2560623248","https://openalex.org/W2589423112","https://openalex.org/W2767354680","https://openalex.org/W2774738748","https://openalex.org/W2807853761","https://openalex.org/W2889555425","https://openalex.org/W2910318997","https://openalex.org/W2912171584","https://openalex.org/W2969890559","https://openalex.org/W3001880610","https://openalex.org/W3002363522","https://openalex.org/W3030736818","https://openalex.org/W3045444181","https://openalex.org/W4235295213","https://openalex.org/W4293003482"],"related_works":["https://openalex.org/W4315620549","https://openalex.org/W3045444181","https://openalex.org/W3156085443","https://openalex.org/W2171234651","https://openalex.org/W3201165851","https://openalex.org/W4247366125","https://openalex.org/W7043560864","https://openalex.org/W2098280758","https://openalex.org/W4399661491","https://openalex.org/W1990806874"],"abstract_inverted_index":{"Even":[0],"though":[1],"the":[2,28,31,38,51,55,58,61,68,84,88,93,96,99,119,132,139,142],"first":[3],"docking":[4,109],"procedures":[5],"were":[6],"developed":[7],"almost":[8],"40":[9],"years":[10],"ago,":[11],"they":[12],"are":[13,26,144],"still":[14],"under":[15],"intense":[16],"development,":[17],"alongside":[18],"with":[19],"their":[20,45,65],"validation.":[21],"In":[22,81],"this":[23,82],"article,":[24],"we":[25],"proposing":[27],"use":[29],"of":[30,40,90,101,108,118,121,131],"quantum":[32],"free-orbital":[33],"AlteQ":[34,48,85,133],"method":[35,49,86],"in":[36,54],"evaluating":[37],"correctness":[39],"ligand":[41,59,94,103,140],"binding":[42],"poses":[43],"and":[44,60,63,95,111,128,141],"ranking.":[46],"The":[47],"calculates":[50],"electron":[52],"density":[53],"interspace":[56],"between":[57,92,138],"receptor,":[62,97],"since":[64],"interactions":[66],"follow":[67],"maximum":[69],"complementarity":[70,137],"principle,":[71],"an":[72,116],"equation":[73],"can":[74,112],"be":[75,113],"obtained,":[76],"which":[77],"describes":[78],"these":[79],"interactions.":[80],"way,":[83],"evaluates":[87],"quality":[89],"contacts":[91],"bypasses":[98],"drawbacks":[100],"using":[102],"RMSD":[104],"as":[105,115],"a":[106],"measure":[107],"quality,":[110],"considered":[114],"improvement":[117],"\"fraction":[120],"recovered":[122],"ligand-receptor":[123],"contacts\"":[124],"method.":[125],"Free":[126],"Windows":[127],"Linux":[129],"versions":[130],"program":[134],"for":[135,146],"assessing":[136],"receptor":[143],"available":[145],"download":[147],"at":[148],"www.chemosophia.com.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":4}],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2021-04-13T00:00:00"}