{"id":"https://openalex.org/W2069478010","doi":"https://doi.org/10.1021/ci800154w","title":"Evaluation of Different Virtual Screening Programs for Docking in a Charged Binding Pocket","display_name":"Evaluation of Different Virtual Screening Programs for Docking in a Charged Binding Pocket","publication_year":2008,"publication_date":"2008-09-27","ids":{"openalex":"https://openalex.org/W2069478010","doi":"https://doi.org/10.1021/ci800154w","mag":"2069478010","pmid":"https://pubmed.ncbi.nlm.nih.gov/18821750"},"language":"en","primary_location":{"id":"doi:10.1021/ci800154w","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci800154w","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2761750","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078132630","display_name":"Wei Deng","orcid":"https://orcid.org/0000-0002-5972-560X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Deng","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065096568","display_name":"Christophe L. M. J. Verlinde","orcid":"https://orcid.org/0000-0002-7790-3203"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christophe L. M. J. Verlinde","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5078132630"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":null,"apc_paid":null,"fwci":1.9165,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.85956216,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"48","issue":"10","first_page":"2010","last_page":"2020"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9643999934196472,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9643999934196472,"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/T11159","display_name":"Manufacturing Process and Optimization","score":0.9363999962806702,"subfield":{"id":"https://openalex.org/subfields/2209","display_name":"Industrial and Manufacturing Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10876","display_name":"Fault Detection and Control Systems","score":0.9362000226974487,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7744125127792358},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.7377883195877075},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4773963987827301},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.37572258710861206},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16373589634895325},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.15454664826393127},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.15195614099502563}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7744125127792358},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7377883195877075},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4773963987827301},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37572258710861206},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16373589634895325},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.15454664826393127},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.15195614099502563},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003576","descriptor_name":"Electron Transport Complex IV","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003576","descriptor_name":"Electron Transport Complex IV","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003576","descriptor_name":"Electron Transport Complex IV","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003576","descriptor_name":"Electron Transport Complex IV","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006418","descriptor_name":"Heme","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006418","descriptor_name":"Heme","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006418","descriptor_name":"Heme","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006418","descriptor_name":"Heme","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D011955","descriptor_name":"Receptors, Drug","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011955","descriptor_name":"Receptors, Drug","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011955","descriptor_name":"Receptors, Drug","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011955","descriptor_name":"Receptors, Drug","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci800154w","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci800154w","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:18821750","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18821750","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:pubmedcentral.nih.gov:2761750","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2761750","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:2761750","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2761750","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Clean water and sanitation","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/6"},{"display_name":"Affordable and clean energy","score":0.4300000071525574,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1497828738","https://openalex.org/W1531401772","https://openalex.org/W1536742834","https://openalex.org/W1588174079","https://openalex.org/W1596348044","https://openalex.org/W1964692086","https://openalex.org/W1967809254","https://openalex.org/W1972148009","https://openalex.org/W1973180272","https://openalex.org/W1974809008","https://openalex.org/W1977467384","https://openalex.org/W1978569451","https://openalex.org/W1980285986","https://openalex.org/W1980949045","https://openalex.org/W1983304433","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W1990472384","https://openalex.org/W1993071541","https://openalex.org/W1994067196","https://openalex.org/W1994114759","https://openalex.org/W2000825058","https://openalex.org/W2002755329","https://openalex.org/W2003356525","https://openalex.org/W2008005113","https://openalex.org/W2009423060","https://openalex.org/W2015033725","https://openalex.org/W2031337364","https://openalex.org/W2032946695","https://openalex.org/W2035292911","https://openalex.org/W2037535298","https://openalex.org/W2040163251","https://openalex.org/W2040496005","https://openalex.org/W2042071104","https://openalex.org/W2050456292","https://openalex.org/W2051381895","https://openalex.org/W2052030759","https://openalex.org/W2055410316","https://openalex.org/W2056179306","https://openalex.org/W2056611993","https://openalex.org/W2059890035","https://openalex.org/W2060002448","https://openalex.org/W2062845058","https://openalex.org/W2067455153","https://openalex.org/W2068017935","https://openalex.org/W2068672372","https://openalex.org/W2073410243","https://openalex.org/W2074766125","https://openalex.org/W2074978477","https://openalex.org/W2077332797","https://openalex.org/W2087815530","https://openalex.org/W2091734240","https://openalex.org/W2095501702","https://openalex.org/W2099900074","https://openalex.org/W2102377211","https://openalex.org/W2103300124","https://openalex.org/W2107506448","https://openalex.org/W2111796195","https://openalex.org/W2121895929","https://openalex.org/W2133773344","https://openalex.org/W2137276216","https://openalex.org/W2142820798","https://openalex.org/W2145682943","https://openalex.org/W2158534713","https://openalex.org/W2169984716","https://openalex.org/W2747485148","https://openalex.org/W4296588184"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2336040088"],"abstract_inverted_index":{"Virtual":[0],"screening":[1],"of":[2,19,30,41,81,112,119,125],"small":[3,68],"molecules":[4],"against":[5],"a":[6,23],"protein":[7],"target":[8],"often":[9],"identifies":[10],"the":[11,15,39,59,95,106,129],"correct":[12],"pose,":[13],"but":[14],"ranking":[16],"in":[17,27,62,128],"terms":[18],"binding":[20,97],"energy":[21],"remains":[22],"difficult":[24],"problem,":[25,38],"resulting":[26],"unacceptable":[28],"numbers":[29],"false":[31],"positives":[32],"and":[33,47,73,89,109,123],"negatives.":[34],"To":[35],"investigate":[36],"this":[37],"performance":[40,102],"three":[42],"docking":[43,100],"programs,":[44],"FRED,":[45],"QXP/FLO,":[46],"GLIDE,":[48],"along":[49],"with":[50,58,94],"their":[51,110],"five":[52],"different":[53,120],"scoring":[54],"functions,":[55],"was":[56],"evaluated":[57],"engineered":[60],"cavity":[61,69,130],"cytochrome":[63],"c":[64],"peroxidase":[65],"(CCP).":[66],"This":[67],"is":[70,103],"negatively":[71],"charged":[72],"completely":[74],"buried":[75],"from":[76,117],"solvent.":[77],"A":[78],"test":[79],"set":[80],"60":[82],"molecules,":[83],"experimentally":[84],"identified":[85],"as":[86],"43":[87],"\"binders\"":[88],"17":[90],"\"non-binders\",":[91],"were":[92],"tested":[93],"CCP":[96],"site.":[98],"The":[99,115],"methods'":[101],"quantified":[104],"by":[105],"ROC":[107],"curve":[108],"reproduction":[111],"crystal":[113],"poses.":[114],"effects":[116],"generation":[118],"ligand":[121],"tautomers":[122],"inclusion":[124],"water":[126],"molecule":[127],"are":[131],"also":[132],"discussed.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
