{"id":"https://openalex.org/W2031153203","doi":"https://doi.org/10.1021/ci200078f","title":"Support Vector Regression Scoring of Receptor\u2013Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries","display_name":"Support Vector Regression Scoring of Receptor\u2013Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries","publication_year":2011,"publication_date":"2011-07-05","ids":{"openalex":"https://openalex.org/W2031153203","doi":"https://doi.org/10.1021/ci200078f","mag":"2031153203","pmid":"https://pubmed.ncbi.nlm.nih.gov/21728360"},"language":"en","primary_location":{"id":"doi:10.1021/ci200078f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200078f","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/A5103403456","display_name":"Liwei Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Liwei Li","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100408160","display_name":"Bo Wang","orcid":"https://orcid.org/0000-0002-9620-3413"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Indiana University\u2212Purdue University, Indianapolis, Indiana, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Indiana University\u2212Purdue University, Indianapolis, Indiana, United States","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055133888","display_name":"Samy O. Meroueh","orcid":"https://orcid.org/0000-0002-3948-7499"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samy O. Meroueh","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Indiana University\u2212Purdue University, Indianapolis, Indiana, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Indiana University\u2212Purdue University, Indianapolis, Indiana, United States","institution_ids":["https://openalex.org/I55769427"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103403456"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.8503,"has_fulltext":false,"cited_by_count":104,"citation_normalized_percentile":{"value":0.96563181,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"51","issue":"9","first_page":"2132","last_page":"2138"},"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":0.9961000084877014,"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":0.9758999943733215,"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/support-vector-machine","display_name":"Support vector machine","score":0.8735533952713013},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.7043603658676147},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5702967643737793},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5689774751663208},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.5293912291526794},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4652802348136902},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46454906463623047},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.4516259729862213},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.4355345666408539},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.42349156737327576},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.42240551114082336},{"id":"https://openalex.org/keywords/spearmans-rank-correlation-coefficient","display_name":"Spearman's rank correlation coefficient","score":0.42037373781204224},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40246689319610596},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3519335389137268},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1972370445728302},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1273227035999298},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07492870092391968}],"concepts":[{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.8735533952713013},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7043603658676147},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5702967643737793},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5689774751663208},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.5293912291526794},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4652802348136902},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46454906463623047},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.4516259729862213},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.4355345666408539},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.42349156737327576},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.42240551114082336},{"id":"https://openalex.org/C159744936","wikidata":"https://www.wikidata.org/wiki/Q1126730","display_name":"Spearman's rank correlation coefficient","level":2,"score":0.42037373781204224},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40246689319610596},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3519335389137268},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1972370445728302},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1273227035999298},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07492870092391968},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","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},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/ci200078f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200078f","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:21728360","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21728360","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:2449789","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3209528","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"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/49884","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/49884","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307904","display_name":"Oracle","ror":"https://ror.org/006c77m33"},{"id":"https://openalex.org/F4320309409","display_name":"Lilly Endowment","ror":"https://ror.org/00cpsd622"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1512801428","https://openalex.org/W1539947917","https://openalex.org/W1592950931","https://openalex.org/W1605578858","https://openalex.org/W1979914800","https://openalex.org/W1995852445","https://openalex.org/W2001722230","https://openalex.org/W2001816314","https://openalex.org/W2009423060","https://openalex.org/W2012084558","https://openalex.org/W2014276094","https://openalex.org/W2014967718","https://openalex.org/W2015461838","https://openalex.org/W2019118901","https://openalex.org/W2021204780","https://openalex.org/W2023856915","https://openalex.org/W2036350498","https://openalex.org/W2059885812","https://openalex.org/W2074978477","https://openalex.org/W2087359404","https://openalex.org/W2092285329","https://openalex.org/W2098312592","https://openalex.org/W2111078532","https://openalex.org/W2127760066","https://openalex.org/W2128332459","https://openalex.org/W2134967712","https://openalex.org/W2146465875","https://openalex.org/W2148512505","https://openalex.org/W2202155158"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2807634898","https://openalex.org/W1692008701","https://openalex.org/W2942366970","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2714724074"],"abstract_inverted_index":{"The":[0,50],"community":[1],"structure-activity":[2],"resource":[3],"(CSAR)":[4],"data":[5,48,102],"sets":[6],"are":[7,29,56],"used":[8,52,76],"to":[9,53,72,177,197],"develop":[10],"and":[11,27,68,86,123,192],"test":[12],"a":[13,159,168,182],"support":[14],"vector":[15],"machine-based":[16],"scoring":[17,24,77,107,189,201],"function":[18,202],"in":[19,131,140,195],"regression":[20],"mode":[21],"(SVR).":[22],"Two":[23],"functions":[25,190],"(SVR-KB":[26],"SVR-EP)":[28],"derived":[30,200],"with":[31,93],"the":[32,36,39,45,100,145,149],"objective":[33],"of":[34,38,99,148,151,161],"reproducing":[35],"trend":[37],"experimental":[40],"binding":[41],"affinities":[42],"provided":[43],"within":[44],"two":[46],"CSAR":[47],"sets.":[49],"features":[51,94],"train":[54],"SVR-KB":[55,67,91,162],"knowledge-based":[57],"pairwise":[58],"potentials,":[59],"while":[60],"SVR-EP":[61,69],"is":[62],"based":[63],"on":[64],"physicochemical":[65],"properties.":[66],"were":[70],"compared":[71],"seven":[73],"other":[74,106,188],"widely":[75],"functions,":[78,108],"including":[79,109],"Glide,":[80],"X-score,":[81,112],"GoldScore,":[82],"ChemScore,":[83],"Vina,":[84],"Dock,":[85],"PMF.":[87],"Results":[88],"showed":[89,181],"that":[90,128,172],"trained":[92],"obtained":[95],"from":[96],"three-dimensional":[97],"complexes":[98],"PDBbind":[101],"set":[103],"outperformed":[104],"all":[105,187],"best":[110],"performing":[111],"by":[113,166],"nearly":[114],"0.1":[115],"using":[116,144],"three":[117],"correlation":[118],"coefficients,":[119],"namely":[120],"Pearson,":[121],"Spearman,":[122],"Kendall.":[124],"It":[125],"was":[126,164,193],"interesting":[127],"higher":[129,184],"performance":[130,196],"rank":[132],"ordering":[133],"did":[134],"not":[135],"translate":[136],"into":[137],"greater":[138],"enrichment":[139],"virtual":[141],"screening":[142],"assessed":[143],"40":[146],"targets":[147],"Directory":[150],"Useful":[152],"Decoys":[153],"(DUD).":[154],"To":[155],"remedy":[156],"this":[157],"situation,":[158],"variant":[160],"(SVR-KBD)":[163],"developed":[165],"following":[167],"target-specific":[169],"tailoring":[170],"strategy":[171],"we":[173],"had":[174],"previously":[175,199],"employed":[176],"derive":[178],"SVM-SP.":[179,203],"SVR-KBD":[180],"much":[183],"enrichment,":[185],"outperforming":[186],"tested,":[191],"comparable":[194],"our":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
