{"id":"https://openalex.org/W1503377786","doi":"https://doi.org/10.22146/ijc.21245","title":"Retrospective Validation of a Structure-Based Virtual Screening Protocol to Identify Ligands for Estrogen Receptor Alpha and Its Application to Identify the Alpha-Mangostin Binding Pose","display_name":"Retrospective Validation of a Structure-Based Virtual Screening Protocol to Identify Ligands for Estrogen Receptor Alpha and Its Application to Identify the Alpha-Mangostin Binding Pose","publication_year":2014,"publication_date":"2014-07-25","ids":{"openalex":"https://openalex.org/W1503377786","doi":"https://doi.org/10.22146/ijc.21245","mag":"1503377786"},"language":"en","primary_location":{"id":"doi:10.22146/ijc.21245","doi":"https://doi.org/10.22146/ijc.21245","is_oa":true,"landing_page_url":"http://doi.org/10.22146/ijc.21245","pdf_url":null,"source":{"id":"https://openalex.org/S2764840418","display_name":"Indonesian Journal of Chemistry","issn_l":"1411-9420","issn":["1411-9420","2460-1578"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj","dongbi-d","poland-40","russia-white-list-3"],"host_organization":"https://openalex.org/P4310314959","host_organization_name":"Gadjah Mada University","host_organization_lineage":["https://openalex.org/P4310314959"],"host_organization_lineage_names":["Gadjah Mada University"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Indonesian Journal of Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://doi.org/10.22146/ijc.21245","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042362319","display_name":"Agustina Setiawati","orcid":"https://orcid.org/0000-0001-6301-3413","observed_orcids":["https://orcid.org/0000-0001-6301-3413"]},"institutions":[{"id":"https://openalex.org/I184925374","display_name":"Sanata Dharma University","ror":"https://ror.org/02105t278","country_code":"ID","type":"education","lineage":["https://openalex.org/I184925374"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Agustina Setiawati","raw_affiliation_strings":["Laboratory of Pharmacognosy-Phytochemistry, Faculty of Pharmacy, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Yogyakarta 55284"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Pharmacognosy-Phytochemistry, Faculty of Pharmacy, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Yogyakarta 55284","institution_ids":["https://openalex.org/I184925374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025928019","display_name":"Florentinus Dika Octa Riswanto","orcid":"https://orcid.org/0000-0002-7174-6382","observed_orcids":["https://orcid.org/0000-0002-7174-6382"]},"institutions":[{"id":"https://openalex.org/I184925374","display_name":"Sanata Dharma University","ror":"https://ror.org/02105t278","country_code":"ID","type":"education","lineage":["https://openalex.org/I184925374"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Florentinus Dika Octa Riswanto","raw_affiliation_strings":["Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Yogyakarta 55284"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Yogyakarta 55284","institution_ids":["https://openalex.org/I184925374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069362130","display_name":"Sri Hartati Yuliani","orcid":"https://orcid.org/0000-0001-5246-8252","observed_orcids":["https://orcid.org/0000-0001-5246-8252"]},"institutions":[{"id":"https://openalex.org/I184925374","display_name":"Sanata Dharma University","ror":"https://ror.org/02105t278","country_code":"ID","type":"education","lineage":["https://openalex.org/I184925374"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Sri Hartati Yuliani","raw_affiliation_strings":["Laboratory of Pharmaceutical Technology, Faculty of Pharmacy, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Yogyakarta 55284"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Pharmaceutical Technology, Faculty of Pharmacy, Sanata Dharma University, Paingan, Maguwoharjo, Depok, Yogyakarta 55284","institution_ids":["https://openalex.org/I184925374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089206830","display_name":"Enade Perdana Istyastono","orcid":"https://orcid.org/0000-0002-8344-5587","observed_orcids":["https://orcid.org/0000-0002-8344-5587"]},"institutions":[{"id":"https://openalex.org/I184925374","display_name":"Sanata Dharma University","ror":"https://ror.org/02105t278","country_code":"ID","type":"education","lineage":["https://openalex.org/I184925374"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Enade Perdana Istyastono","raw_affiliation_strings":["Sanata Dharma University, Yogyakarta, Indonesia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sanata Dharma University, Yogyakarta, Indonesia","institution_ids":["https://openalex.org/I184925374"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I184925374"],"apc_list":{"value":300,"currency":"USD","value_usd":300},"apc_paid":{"value":300,"currency":"USD","value_usd":300},"fwci":1.1211,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.70948663,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":87,"max":97},"biblio":{"volume":"14","issue":"2","first_page":"103","last_page":"108"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12023","display_name":"Cholinesterase and Neurodegenerative Diseases","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/estrogen-receptor-alpha","display_name":"estrogen receptor alpha","score":0.9440000057220459},{"id":"https://openalex.org/keywords/structure-based-virtual-screening","display_name":"structure-based virtual screening","score":0.996999979019165},{"id":"https://openalex.org/keywords/retrospective-validation","display_name":"retrospective validation","score":0.8790000081062317},{"id":"https://openalex.org/keywords/alpha-mangostin","display_name":"\u03b1-mangostin","score":0.8600000143051147},{"id":"https://openalex.org/keywords/binding-poses","display_name":"binding poses","score":0.6629999876022339},{"id":"https://openalex.org/keywords/4-hydroxytamoxifen","display_name":"4-hydroxytamoxifen","score":0.9089999794960022},{"id":"https://openalex.org/keywords/ligand-identification","display_name":"ligand identification","score":0.6890000104904175},{"id":"https://openalex.org/keywords/garcinia-mangostana","display_name":"Garcinia mangostana","score":0.8119999766349792},{"id":"https://openalex.org/keywords/enrichment-factor","display_name":"enrichment factor","score":0.4690000116825104}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7349658012390137},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6913791298866272},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6245827078819275},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.5710899829864502},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4880196154117584},{"id":"https://openalex.org/C172313692","wikidata":"https://www.wikidata.org/wiki/Q14902310","display_name":"Estrogen receptor alpha","level":5,"score":0.4536624550819397},{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.3530772030353546},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3499739170074463},{"id":"https://openalex.org/C84606932","wikidata":"https://www.wikidata.org/wiki/Q416496","display_name":"Estrogen receptor","level":4,"score":0.27470827102661133},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2650412321090698},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.16921153664588928},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15729162096977234},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.08352628350257874},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.08119124174118042},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.0},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.22146/ijc.21245","doi":"https://doi.org/10.22146/ijc.21245","is_oa":true,"landing_page_url":"http://doi.org/10.22146/ijc.21245","pdf_url":null,"source":{"id":"https://openalex.org/S2764840418","display_name":"Indonesian Journal of Chemistry","issn_l":"1411-9420","issn":["1411-9420","2460-1578"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj","dongbi-d","poland-40","russia-white-list-3"],"host_organization":"https://openalex.org/P4310314959","host_organization_name":"Gadjah Mada University","host_organization_lineage":["https://openalex.org/P4310314959"],"host_organization_lineage_names":["Gadjah Mada University"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Indonesian Journal of Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.914.613","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.914.613","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://pdm-mipa.ugm.ac.id/ojs/index.php/ijc/article/download/850/930/","raw_type":"text"},{"id":"pmh:oai:journal.ugm.ac.id:article/21245","doi":null,"is_oa":true,"landing_page_url":"https://journal.ugm.ac.id/ijc/article/view/21245","pdf_url":"https://journal.ugm.ac.id/ijc/article/download/21245/13950","source":{"id":"https://openalex.org/S4306400707","display_name":"Indonesian Journal of Biotechnology (Universitas Gadjah Mada)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I165230279","host_organization_name":"Universitas Gadjah Mada","host_organization_lineage":["https://openalex.org/I165230279"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"1411-9420","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:960d8a6592464891b138e265d4358e9a","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/960d8a6592464891b138e265d4358e9a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Indonesian Journal of Chemistry, Vol 14, Iss 2, Pp 103-108 (2014)","raw_type":"article"},{"id":"pmh:oai:jurnal.ugm.ac.id:article/21245","doi":null,"is_oa":true,"landing_page_url":"http://jurnal.ugm.ac.id/ijc/article/view/21245","pdf_url":null,"source":{"id":"https://openalex.org/S4306400707","display_name":"Indonesian Journal of Biotechnology (Universitas Gadjah Mada)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I165230279","host_organization_name":"Universitas Gadjah Mada","host_organization_lineage":["https://openalex.org/I165230279"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Indonesian Journal of Chemistry; Vol 14, No 2 (2014); 103-108","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.22146/ijc.21245","doi":"https://doi.org/10.22146/ijc.21245","is_oa":true,"landing_page_url":"http://doi.org/10.22146/ijc.21245","pdf_url":null,"source":{"id":"https://openalex.org/S2764840418","display_name":"Indonesian Journal of Chemistry","issn_l":"1411-9420","issn":["1411-9420","2460-1578"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj","dongbi-d","poland-40","russia-white-list-3"],"host_organization":"https://openalex.org/P4310314959","host_organization_name":"Gadjah Mada University","host_organization_lineage":["https://openalex.org/P4310314959"],"host_organization_lineage_names":["Gadjah Mada University"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Indonesian Journal of Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.46810001134872437,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1503377786.pdf","grobid_xml":"https://content.openalex.org/works/W1503377786.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W2047409016","https://openalex.org/W2195116424"],"related_works":["https://openalex.org/W2221625447","https://openalex.org/W2897797380","https://openalex.org/W131425331","https://openalex.org/W2229073095","https://openalex.org/W2031480738","https://openalex.org/W2794909421","https://openalex.org/W2794571810","https://openalex.org/W2036100857","https://openalex.org/W3097733972","https://openalex.org/W2078371139"],"abstract_inverted_index":{"The":[0,60],"publicly":[1],"available":[2],"enhanced":[3],"data":[4],"of":[5,23,44,79,104,135,149],"ligands":[6,32,122],"and":[7,72],"decoys":[8],"for":[9,33,123],"estrogen":[10],"receptor":[11],"alpha":[12],"(ER\u03b1)":[13],"which":[14],"were":[15],"recently":[16],"published":[17,89],"has":[18],"made":[19],"the":[20,41,57,73,80,87,97,101,113,139,146,156],"retrospective":[21,42],"validation":[22,43],"a":[24],"structure-based":[25],"virtual":[26],"screening":[27],"(SBVS)":[28],"protocol":[29,47,61,98,114,140],"to":[30,86,119,128,144],"identify":[31,120],"ER\u03b1":[34,107,124,152],"possible.":[35],"In":[36],"this":[37],"article,":[38],"we":[39],"present":[40],"an":[45,151],"SBVS":[46],"using":[48],"PLANTS":[49],"molecular":[50],"docking":[51],"software":[52],"version":[53],"1.2":[54],"(PLANTS1.2)":[55],"as":[56],"backbone":[58],"software.":[59],"shows":[62,111],"better":[63],"enrichment":[64],"factor":[65],"at":[66],"1%":[67],"false":[68],"positives":[69],"(EF1%)":[70],"value":[71,78],"Area":[74],"Under":[75],"Curve":[76],"(AUC)":[77],"Receiver":[81],"Operator":[82],"Characteristic":[83],"(ROC)":[84],"compared":[85],"original":[88],"protocol.":[90],"Moreover,":[91],"in":[92,106,131,155],"all":[93],"1000":[94],"iterative":[95],"attempts":[96],"could":[99],"reproduce":[100],"co-crystal":[102],"pose":[103,134],"4-hydroxitamoxifen":[105],"binding":[108,133,147],"pocket.":[109],"It":[110],"that":[112],"is":[115],"not":[116],"only":[117],"able":[118,127],"potent":[121],"but":[125],"also":[126],"be":[129],"employed":[130,143],"examining":[132],"known":[136],"ligand.":[137],"Thence,":[138],"was":[141],"successfully":[142],"examine":[145],"poses":[148],"\u03b1-mangostin,":[150],"ligand":[153],"found":[154],"Garcinia":[157],"mangostana,":[158],"L.":[159],"pericarp.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}