{"id":"https://openalex.org/W1974734322","doi":"https://doi.org/10.1021/ci300411b","title":"Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines","display_name":"Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines","publication_year":2012,"publication_date":"2012-11-03","ids":{"openalex":"https://openalex.org/W1974734322","doi":"https://doi.org/10.1021/ci300411b","mag":"1974734322"},"language":"en","primary_location":{"id":"doi:10.1021/ci300411b","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300411b","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"],"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/A5037007489","display_name":"Thijs Beuming","orcid":"https://orcid.org/0000-0002-5991-7118"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thijs Beuming","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 120 West 45th Street, New York, New York, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 120 West 45th Street, New York, New York, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087455853","display_name":"Woody Sherman","orcid":"https://orcid.org/0000-0001-9079-1376"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Woody Sherman","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 120 West 45th Street, New York, New York, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 120 West 45th Street, New York, New York, United States","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037007489"],"corresponding_institution_ids":["https://openalex.org/I203455613"],"apc_list":null,"apc_paid":null,"fwci":5.7788,"has_fulltext":false,"cited_by_count":92,"citation_normalized_percentile":{"value":0.97057746,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"52","issue":"12","first_page":"3263","last_page":"3277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":1.0,"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":1.0,"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/T10814","display_name":"Neuropeptides and Animal Physiology","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.8517554998397827},{"id":"https://openalex.org/keywords/g-protein-coupled-receptor","display_name":"G protein-coupled receptor","score":0.834805965423584},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.7430704236030579},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6034755110740662},{"id":"https://openalex.org/keywords/agonist","display_name":"Agonist","score":0.5219642519950867},{"id":"https://openalex.org/keywords/dock","display_name":"DOCK","score":0.5013206005096436},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.49466559290885925},{"id":"https://openalex.org/keywords/modeller","display_name":"MODELLER","score":0.43584007024765015},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43505001068115234},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3490760326385498},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3256221413612366},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.25460654497146606},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.14770227670669556},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.07647693157196045}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8517554998397827},{"id":"https://openalex.org/C135285700","wikidata":"https://www.wikidata.org/wiki/Q38173","display_name":"G protein-coupled receptor","level":3,"score":0.834805965423584},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.7430704236030579},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6034755110740662},{"id":"https://openalex.org/C2778938600","wikidata":"https://www.wikidata.org/wiki/Q389934","display_name":"Agonist","level":3,"score":0.5219642519950867},{"id":"https://openalex.org/C93073132","wikidata":"https://www.wikidata.org/wiki/Q24726581","display_name":"DOCK","level":2,"score":0.5013206005096436},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.49466559290885925},{"id":"https://openalex.org/C193153401","wikidata":"https://www.wikidata.org/wiki/Q3859815","display_name":"MODELLER","level":4,"score":0.43584007024765015},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43505001068115234},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3490760326385498},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3256221413612366},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25460654497146606},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14770227670669556},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.07647693157196045},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1021/ci300411b","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300411b","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"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7099999785423279}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W1833104430","https://openalex.org/W1908561802","https://openalex.org/W1965822917","https://openalex.org/W1969027187","https://openalex.org/W1971652848","https://openalex.org/W1973228989","https://openalex.org/W1975570414","https://openalex.org/W1975691556","https://openalex.org/W1975740938","https://openalex.org/W1976975058","https://openalex.org/W1979166300","https://openalex.org/W1980962873","https://openalex.org/W1984291348","https://openalex.org/W1985588649","https://openalex.org/W1988477436","https://openalex.org/W1989971979","https://openalex.org/W1995808589","https://openalex.org/W1995850373","https://openalex.org/W2006185600","https://openalex.org/W2009423060","https://openalex.org/W2014055152","https://openalex.org/W2020601776","https://openalex.org/W2021750784","https://openalex.org/W2025458374","https://openalex.org/W2026501736","https://openalex.org/W2034266737","https://openalex.org/W2041566506","https://openalex.org/W2042170152","https://openalex.org/W2043209972","https://openalex.org/W2046274153","https://openalex.org/W2047144511","https://openalex.org/W2048718061","https://openalex.org/W2050366220","https://openalex.org/W2051106500","https://openalex.org/W2060874643","https://openalex.org/W2063273962","https://openalex.org/W2063535987","https://openalex.org/W2079953901","https://openalex.org/W2080231167","https://openalex.org/W2083394907","https://openalex.org/W2083725367","https://openalex.org/W2089969245","https://openalex.org/W2102377211","https://openalex.org/W2102513649","https://openalex.org/W2104961861","https://openalex.org/W2109014958","https://openalex.org/W2117003397","https://openalex.org/W2122434726","https://openalex.org/W2123563726","https://openalex.org/W2127739127","https://openalex.org/W2130813862","https://openalex.org/W2133773344","https://openalex.org/W2137015675","https://openalex.org/W2140690192","https://openalex.org/W2142322475","https://openalex.org/W2143482176","https://openalex.org/W2149963584","https://openalex.org/W2151784842","https://openalex.org/W2152853006","https://openalex.org/W2167086539","https://openalex.org/W2167857702","https://openalex.org/W2168833646","https://openalex.org/W2411751083","https://openalex.org/W6907608579","https://openalex.org/W6963796733"],"related_works":["https://openalex.org/W4282913408","https://openalex.org/W2100436540","https://openalex.org/W2300502530","https://openalex.org/W3201417569","https://openalex.org/W3033824302","https://openalex.org/W2070163817","https://openalex.org/W2102475066","https://openalex.org/W2395175315","https://openalex.org/W1600721761","https://openalex.org/W1938743025"],"abstract_inverted_index":{"The":[0,64],"growing":[1],"availability":[2],"of":[3,20,26,34,37,72,86,131,138,154,157],"novel":[4],"structures":[5,43,71,85],"for":[6,16,79,103],"several":[7],"G":[8],"protein-coupled":[9],"receptors":[10,123],"(GPCRs)":[11],"has":[12],"provided":[13],"new":[14],"opportunities":[15],"structure-based":[17],"drug":[18],"design":[19],"ligands":[21,68,139],"against":[22],"this":[23],"important":[24],"class":[25],"targets.":[27],"Here,":[28],"we":[29,98],"report":[30],"a":[31],"systematic":[32],"analysis":[33],"the":[35,73,87,91,104,129,135,148,152,155,160],"accuracy":[36,150],"docking":[38,132,149,166],"small":[39],"molecules":[40],"into":[41,69],"GPCR":[42],"and":[44,53,56,82,90,93,119,127,151],"homology":[45,101],"models":[46,102],"using":[47,124],"both":[48,80],"rigid":[49],"receptor":[50,58,89],"(Glide":[51],"SP":[52],"Glide":[54],"XP)":[55],"flexible":[57],"(Induced":[59],"Fit":[60],"Docking;":[61],"IFD)":[62],"methods.":[63],"ability":[65,130],"to":[66,133,159],"dock":[67],"different":[70],"same":[74],"target":[75],"(cross-docking)":[76],"is":[77],"evaluated":[78],"agonist":[81,84],"inverse":[83],"A2A":[88,115],"\u03b21-":[92],"\u03b22-adrenergic":[94],"receptors.":[95],"In":[96],"addition,":[97],"have":[99],"produced":[100],"\u03b21-adrenergic,":[105],"\u03b22-adrenergic,":[106],"D3":[107],"dopamine,":[108],"H1":[109],"histamine,":[110],"M2":[111],"muscarine,":[112,114],"M3":[113],"adenosine,":[116],"S1P1,":[117],"\u03ba-opioid,":[118],"C-X-C":[120],"chemokine":[121],"4":[122],"multiple":[125],"templates":[126],"investigated":[128],"predict":[134],"binding":[136,171],"mode":[137],"in":[140,164],"these":[141],"models.":[142],"Clear":[143],"correlations":[144],"are":[145],"observed":[146],"between":[147],"similarity":[153],"sequence":[156],"interest":[158],"template,":[161],"suggesting":[162],"regimes":[163],"which":[165],"can":[167],"correctly":[168],"identify":[169],"ligand":[170],"modes.":[172]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":15},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":18},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
