{"id":"https://openalex.org/W2077417417","doi":"https://doi.org/10.1021/ci200080g","title":"Construction and Test of Ligand Decoy Sets Using MDock: Community Structure\u2013Activity Resource Benchmarks for Binding Mode Prediction","display_name":"Construction and Test of Ligand Decoy Sets Using MDock: Community Structure\u2013Activity Resource Benchmarks for Binding Mode Prediction","publication_year":2011,"publication_date":"2011-07-14","ids":{"openalex":"https://openalex.org/W2077417417","doi":"https://doi.org/10.1021/ci200080g","mag":"2077417417","pmid":"https://pubmed.ncbi.nlm.nih.gov/21755952"},"language":"en","primary_location":{"id":"doi:10.1021/ci200080g","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200080g","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/A5053305024","display_name":"Sheng\u2010You Huang","orcid":"https://orcid.org/0000-0002-4209-4565"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sheng-You Huang","raw_affiliation_strings":["Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081082371","display_name":"Xiaoqin Zou","orcid":"https://orcid.org/0000-0003-0637-8648"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoqin Zou","raw_affiliation_strings":["Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States","Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053305024"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":2.1969,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.87503352,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"51","issue":"9","first_page":"2107","last_page":"2114"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9972000122070312,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9836999773979187,"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/decoy","display_name":"Decoy","score":0.9646366834640503},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5701172351837158},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5518817901611328},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5063244104385376},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5040382742881775},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4875278174877167},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46049052476882935},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.4135902523994446},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3826243281364441},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32621675729751587},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31298816204071045},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25071099400520325},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1427360475063324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12059500813484192},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.0994960367679596},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.0984741747379303},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09152084589004517}],"concepts":[{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.9646366834640503},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5701172351837158},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5518817901611328},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5063244104385376},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5040382742881775},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4875278174877167},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46049052476882935},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.4135902523994446},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3826243281364441},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32621675729751587},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31298816204071045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25071099400520325},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1427360475063324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12059500813484192},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0994960367679596},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0984741747379303},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09152084589004517},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci200080g","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200080g","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:21755952","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21755952","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:europepmc.org:2449786","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3190646","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1592950931","https://openalex.org/W1972148009","https://openalex.org/W1986568494","https://openalex.org/W2001816314","https://openalex.org/W2005817231","https://openalex.org/W2008517160","https://openalex.org/W2012084558","https://openalex.org/W2015080758","https://openalex.org/W2035292911","https://openalex.org/W2037535298","https://openalex.org/W2038542598","https://openalex.org/W2040496005","https://openalex.org/W2044098211","https://openalex.org/W2048739031","https://openalex.org/W2055410316","https://openalex.org/W2056179306","https://openalex.org/W2058433776","https://openalex.org/W2067455153","https://openalex.org/W2072180710","https://openalex.org/W2072683434","https://openalex.org/W2098971704","https://openalex.org/W2103994532","https://openalex.org/W2105527266","https://openalex.org/W2107506448","https://openalex.org/W2111767148","https://openalex.org/W2115256962","https://openalex.org/W2118233996","https://openalex.org/W2121895929","https://openalex.org/W2124074156","https://openalex.org/W2127760066","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2133773344","https://openalex.org/W2167041509","https://openalex.org/W2169562071","https://openalex.org/W2171234651"],"related_works":["https://openalex.org/W2415073839","https://openalex.org/W1555596338","https://openalex.org/W1238053778","https://openalex.org/W2350944221","https://openalex.org/W4239355779","https://openalex.org/W2124981562","https://openalex.org/W2187341605","https://openalex.org/W3005094479","https://openalex.org/W1973364873","https://openalex.org/W1963920545"],"abstract_inverted_index":{"Two":[0],"sets":[1,65,119],"of":[2,49,69,81,97,128],"ligand":[3,62],"binding":[4,41,51,63,72,113,125],"decoys":[5,30,86],"have":[6,57],"been":[7,58],"constructed":[8],"for":[9,23,32,66,83,89,124],"the":[10,18,36,40,61,84,90,94,107,111,136],"community":[11],"structure-activity":[12],"resource":[13],"(CSAR)":[14],"benchmark":[15,37],"by":[16],"using":[17,60],"MDock":[19],"and":[20,25,43,87],"DOCK":[21],"programs":[22],"rigid-":[24],"flexible-ligand":[26,91],"docking,":[27],"respectively.":[28],"The":[29,117],"generated":[31],"each":[33],"complex":[34],"in":[35],"thoroughly":[38],"cover":[39],"site":[42,139],"also":[44],"contain":[45],"a":[46,78,98,129],"certain":[47],"number":[48],"near-native":[50,71],"modes.":[52,73],"A":[53],"few":[54],"scoring":[55,130],"functions":[56],"evaluated":[59],"decoy":[64,118],"their":[67],"abilities":[68],"predicting":[70],"Among":[74],"them,":[75],"ITScore":[76],"achieved":[77],"success":[79],"rate":[80],"86.7%":[82],"rigid-ligand":[85],"79.7%":[88],"decoys,":[92],"under":[93],"common":[95],"definition":[96],"successful":[99],"prediction":[100,127],"as":[101,122],"root-mean-square":[102],"deviation":[103],"<2.0":[104],"\u00c5":[105],"from":[106],"native":[108],"structure":[109],"if":[110],"top-scored":[112],"mode":[114,126],"was":[115],"considered.":[116],"may":[120],"serve":[121],"benchmarks":[123],"function,":[131],"which":[132],"are":[133],"available":[134],"at":[135],"CSAR":[137],"Web":[138],"(":[140],"http://www.csardock.org/).":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
