{"id":"https://openalex.org/W2001137100","doi":"https://doi.org/10.1021/ci500499j","title":"Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening","display_name":"Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening","publication_year":2014,"publication_date":"2014-10-28","ids":{"openalex":"https://openalex.org/W2001137100","doi":"https://doi.org/10.1021/ci500499j","mag":"2001137100","pmid":"https://pubmed.ncbi.nlm.nih.gov/25350693"},"language":"en","primary_location":{"id":"doi:10.1021/ci500499j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500499j","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/A5112631909","display_name":"Miwa Sato","orcid":null},"institutions":[{"id":"https://openalex.org/I4210118089","display_name":"Mitsui (Japan)","ror":"https://ror.org/01qw4g764","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210118089"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I89630735","display_name":"Yokohama City University","ror":"https://ror.org/0135d1r83","country_code":"JP","type":"education","lineage":["https://openalex.org/I89630735"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Miwa Sato","raw_affiliation_strings":["Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan","Mitsui Knowledge Industry Co., Ltd., Tokyo 105-6215, Japan","Molecular Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan","Department#R#of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan","Molecular#R#Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan","institution_ids":["https://openalex.org/I89630735"]},{"raw_affiliation_string":"Mitsui Knowledge Industry Co., Ltd., Tokyo 105-6215, Japan","institution_ids":["https://openalex.org/I4210118089"]},{"raw_affiliation_string":"Molecular Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Department#R#of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan","institution_ids":["https://openalex.org/I89630735"]},{"raw_affiliation_string":"Molecular#R#Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027918582","display_name":"Takatsugu Hirokawa","orcid":"https://orcid.org/0000-0002-3180-5050"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takatsugu Hirokawa","raw_affiliation_strings":["Molecular Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan","Molecular#R#Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan"],"affiliations":[{"raw_affiliation_string":"Molecular Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Molecular#R#Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5112631909"],"corresponding_institution_ids":["https://openalex.org/I4210118089","https://openalex.org/I73613424","https://openalex.org/I89630735"],"apc_list":null,"apc_paid":null,"fwci":0.8366,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.71472909,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"54","issue":"11","first_page":"3153","last_page":"3161"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9998000264167786,"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"}},{"id":"https://openalex.org/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9811999797821045,"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"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9728000164031982,"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/virtual-screening","display_name":"Virtual screening","score":0.7099836468696594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5714907646179199},{"id":"https://openalex.org/keywords/g-protein-coupled-receptor","display_name":"G protein-coupled receptor","score":0.5175827741622925},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45616963505744934},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41636043787002563},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3309277892112732},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24392199516296387},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.22362831234931946},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20542120933532715},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14902621507644653},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.08600273728370667},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06609323620796204}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7099836468696594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5714907646179199},{"id":"https://openalex.org/C135285700","wikidata":"https://www.wikidata.org/wiki/Q38173","display_name":"G protein-coupled receptor","level":3,"score":0.5175827741622925},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45616963505744934},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41636043787002563},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3309277892112732},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24392199516296387},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.22362831234931946},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20542120933532715},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14902621507644653},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.08600273728370667},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06609323620796204}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci500499j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500499j","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:25350693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25350693","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}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1603274157","https://openalex.org/W1891097825","https://openalex.org/W1960800354","https://openalex.org/W1969343753","https://openalex.org/W1970613671","https://openalex.org/W1977992545","https://openalex.org/W1985588649","https://openalex.org/W1986329744","https://openalex.org/W1988037271","https://openalex.org/W1988074381","https://openalex.org/W1989225023","https://openalex.org/W1993216479","https://openalex.org/W1998273363","https://openalex.org/W2005174659","https://openalex.org/W2005997645","https://openalex.org/W2007117037","https://openalex.org/W2008073909","https://openalex.org/W2008728387","https://openalex.org/W2009423060","https://openalex.org/W2013325166","https://openalex.org/W2028645925","https://openalex.org/W2036833206","https://openalex.org/W2043209972","https://openalex.org/W2048302799","https://openalex.org/W2052029379","https://openalex.org/W2055672066","https://openalex.org/W2060874643","https://openalex.org/W2065283382","https://openalex.org/W2068487566","https://openalex.org/W2069978572","https://openalex.org/W2074599713","https://openalex.org/W2078534481","https://openalex.org/W2081912151","https://openalex.org/W2083394907","https://openalex.org/W2102809572","https://openalex.org/W2104961861","https://openalex.org/W2110252279","https://openalex.org/W2110585820","https://openalex.org/W2114650590","https://openalex.org/W2119692371","https://openalex.org/W2127760066","https://openalex.org/W2133402952","https://openalex.org/W2140690192","https://openalex.org/W2146933058","https://openalex.org/W2150934225","https://openalex.org/W2152853006","https://openalex.org/W2157558738","https://openalex.org/W2159718916","https://openalex.org/W2176516200"],"related_works":["https://openalex.org/W2609050007","https://openalex.org/W3180887190","https://openalex.org/W3011298851","https://openalex.org/W2320211095","https://openalex.org/W4224216382","https://openalex.org/W3195483439","https://openalex.org/W2308164565","https://openalex.org/W2169619547","https://openalex.org/W1570378576","https://openalex.org/W1566559296"],"abstract_inverted_index":{"G-protein-coupled":[0],"receptors":[1],"(GPCRs)":[2],"are":[3,54,62],"a":[4,109,128,184],"pharmaceutically":[5],"important":[6],"protein":[7],"family":[8],"because":[9],"they":[10],"mediate":[11],"numerous":[12],"physiological":[13],"functions.":[14],"The":[15,120],"crystal":[16],"structures":[17,61,168,198],"of":[18,45,69,86,122,141,155],"several":[19],"GPCR":[20,58],"subtypes":[21],"have":[22,92],"been":[23],"determined":[24],"recently,":[25],"encouraging":[26],"efforts":[27],"to":[28,40,77,115,163,183],"apply":[29],"structure-based":[30],"virtual":[31,37,129],"screening":[32,38,130],"(SBVS)":[33],"along":[34],"with":[35,132,166,186,203],"ligand-based":[36],"(LBVS)":[39],"improve":[41],"the":[42,67,84,123,139,142,146,153],"hit":[43],"rate":[44],"active":[46,134],"ligands":[47,135],"from":[48,72,152],"large":[49],"chemical":[50],"libraries.":[51],"Three-dimensional":[52],"models":[53,124],"also":[55],"necessary":[56],"for":[57,79,103],"targets":[59,165],"whose":[60],"unknown.":[63],"Current":[64],"challenges":[65],"include":[66],"selection":[68],"structural":[70],"templates":[71],"available":[73],"structurally":[74],"known":[75,133,167],"GPCRs":[76],"use":[78],"accurate":[80],"modeling":[81,99,118],"and":[82,94,100,136,138,177,182],"understanding":[83],"diversity":[85],"sites":[87],"recognizing":[88],"distinct":[89],"ligands.":[90],"We":[91],"developed":[93],"validated":[95],"an":[96,187],"extended":[97],"template-based":[98,117],"evaluation":[101],"method":[102],"SBVS.":[104],"Models":[105],"were":[106,207],"generated":[107],"using":[108,127,145],"fragmental":[110],"template":[111],"procedure":[112],"in":[113],"addition":[114],"typical":[116],"methods.":[119],"reliability":[121],"was":[125,161],"evaluated":[126],"test":[131],"decoys":[137],"consensus":[140,204],"binding":[143,205],"mode":[144,206],"protein-ligand":[147],"interaction":[148],"fingerprint":[149],"(PLIF)":[150],"derived":[151],"results":[154],"docking":[156],"simulations.":[157],"This":[158],"novel":[159],"workflow":[160],"applied":[162],"three":[164],"(human":[169,190],"dopamine":[170],"receptor":[171],"3,":[172],"human":[173,178],"histamine":[174],"H1":[175],"receptor,":[176],"delta":[179],"opioid":[180],"receptor)":[181],"target":[185],"unknown":[188],"structure":[189],"serotonin":[191],"2A":[192],"receptor).":[193],"In":[194],"each":[195],"case,":[196],"model":[197],"having":[199],"high":[200],"ligand":[201],"selectivity":[202],"generated.":[208]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
