{"id":"https://openalex.org/W2044098211","doi":"https://doi.org/10.1021/ci2000727","title":"Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function","display_name":"Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function","publication_year":2011,"publication_date":"2011-08-10","ids":{"openalex":"https://openalex.org/W2044098211","doi":"https://doi.org/10.1021/ci2000727","mag":"2044098211","pmid":"https://pubmed.ncbi.nlm.nih.gov/21830787"},"language":"en","primary_location":{"id":"doi:10.1021/ci2000727","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci2000727","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":2.993,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.91628209,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"51","issue":"9","first_page":"2097","last_page":"2106"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10906","display_name":"AI-based Problem Solving and Planning","score":0.9067999720573425,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10906","display_name":"AI-based Problem Solving and Planning","score":0.9067999720573425,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/benchmark","display_name":"Benchmark (surveying)","score":0.7257184982299805},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5946496725082397},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5339326858520508},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4705253839492798},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.459372878074646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19256845116615295},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.07107451558113098}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7257184982299805},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5946496725082397},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5339326858520508},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4705253839492798},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.459372878074646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19256845116615295},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.07107451558113098},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003460","descriptor_name":"Crystallization","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":"D008024","descriptor_name":"Ligands","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":"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":"D011485","descriptor_name":"Protein Binding","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci2000727","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci2000727","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:21830787","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21830787","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:2449787","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3190652","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":[{"id":"https://metadata.un.org/sdg/17","score":0.4000000059604645,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309568","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":83,"referenced_works":["https://openalex.org/W69176903","https://openalex.org/W1255705275","https://openalex.org/W1573009101","https://openalex.org/W1579594936","https://openalex.org/W1589812083","https://openalex.org/W1656114533","https://openalex.org/W1965207004","https://openalex.org/W1967348240","https://openalex.org/W1967809254","https://openalex.org/W1972148009","https://openalex.org/W1973098530","https://openalex.org/W1975017420","https://openalex.org/W1980285986","https://openalex.org/W1981161260","https://openalex.org/W1988478019","https://openalex.org/W1989824508","https://openalex.org/W1992583240","https://openalex.org/W1993046136","https://openalex.org/W2003356525","https://openalex.org/W2005817231","https://openalex.org/W2009507474","https://openalex.org/W2009529127","https://openalex.org/W2012084558","https://openalex.org/W2014417929","https://openalex.org/W2014704001","https://openalex.org/W2029582401","https://openalex.org/W2031259080","https://openalex.org/W2032817710","https://openalex.org/W2034192743","https://openalex.org/W2037535298","https://openalex.org/W2038542598","https://openalex.org/W2047730466","https://openalex.org/W2048739031","https://openalex.org/W2051381895","https://openalex.org/W2051419785","https://openalex.org/W2051993924","https://openalex.org/W2052071018","https://openalex.org/W2054394841","https://openalex.org/W2058052041","https://openalex.org/W2060468500","https://openalex.org/W2061079400","https://openalex.org/W2061259478","https://openalex.org/W2072180710","https://openalex.org/W2072683434","https://openalex.org/W2074978477","https://openalex.org/W2080618096","https://openalex.org/W2083497194","https://openalex.org/W2085764610","https://openalex.org/W2087621126","https://openalex.org/W2087928415","https://openalex.org/W2091778154","https://openalex.org/W2092285329","https://openalex.org/W2092443343","https://openalex.org/W2093534098","https://openalex.org/W2094162409","https://openalex.org/W2098312592","https://openalex.org/W2101644302","https://openalex.org/W2105527266","https://openalex.org/W2108695135","https://openalex.org/W2109539263","https://openalex.org/W2110562802","https://openalex.org/W2111767148","https://openalex.org/W2113149246","https://openalex.org/W2114714512","https://openalex.org/W2115318272","https://openalex.org/W2117620409","https://openalex.org/W2118233996","https://openalex.org/W2118587156","https://openalex.org/W2128332459","https://openalex.org/W2130479394","https://openalex.org/W2132262459","https://openalex.org/W2132629607","https://openalex.org/W2135502915","https://openalex.org/W2145682943","https://openalex.org/W2147058445","https://openalex.org/W2155275960","https://openalex.org/W2158360182","https://openalex.org/W2158534713","https://openalex.org/W2169562071","https://openalex.org/W2171234651","https://openalex.org/W2200337275","https://openalex.org/W2411981780","https://openalex.org/W4250659133"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Based":[0],"on":[1,87],"a":[2,10,70,119],"statistical":[3],"mechanics-based":[4],"iterative":[5,29],"method,":[6],"we":[7],"have":[8],"extracted":[9],"set":[11],"of":[12,24,62,73,91,114,118,144],"distance-dependent,":[13],"all-atom":[14],"pairwise":[15],"potentials":[16],"for":[17,141],"protein-ligand":[18,26,65],"interactions":[19],"from":[20],"the":[21,32,54,88,94,101,108,134,142],"crystal":[22],"structures":[23],"1300":[25],"complexes.":[27,66],"The":[28,41,126],"method":[30],"circumvents":[31],"long-standing":[33],"reference":[34],"state":[35],"problem":[36],"in":[37,77],"knowledge-based":[38],"scoring":[39,43,89,99,112,135,145],"functions.":[40,146],"resulted":[42],"function,":[44,100],"referred":[45],"to":[46],"as":[47],"ITScore":[48,67,92],"2.0,":[49,93],"has":[50,84],"been":[51,85],"tested":[52],"with":[53,103],"CSAR":[55],"(Community":[56],"Structure-Activity":[57],"Resource,":[58],"2009":[59],"release)":[60],"benchmark":[61],"345":[63],"diverse":[64],"2.0":[68],"achieved":[69],"Pearson":[71],"correlation":[72],"R(2)":[74],"=":[75],"0.54":[76],"binding":[78],"affinity":[79],"prediction.":[80],"A":[81],"comparative":[82],"analysis":[83],"done":[86],"performances":[90],"van":[95],"der":[96],"Waals":[97],"(VDW)":[98],"VDW":[102,120],"heavy":[104],"atoms":[105],"only,":[106],"and":[107,122],"force":[109],"field":[110],"(FF)":[111],"function":[113],"DOCK":[115],"which":[116,137],"consists":[117],"term":[121],"an":[123],"electrostatic":[124],"term.":[125],"results":[127],"reveal":[128],"several":[129],"important":[130],"factors":[131],"that":[132],"affect":[133],"performances,":[136],"could":[138],"be":[139],"helpful":[140],"improvement":[143]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
