{"id":"https://openalex.org/W2011953761","doi":"https://doi.org/10.1021/ci300154n","title":"GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods","display_name":"GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods","publication_year":2012,"publication_date":"2012-09-12","ids":{"openalex":"https://openalex.org/W2011953761","doi":"https://doi.org/10.1021/ci300154n","mag":"2011953761","pmid":"https://pubmed.ncbi.nlm.nih.gov/22970854"},"language":"en","primary_location":{"id":"doi:10.1021/ci300154n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300154n","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/A5032652911","display_name":"Simon Cross","orcid":"https://orcid.org/0000-0002-8736-4397"},"institutions":[{"id":"https://openalex.org/I4210165610","display_name":"Molecular Discovery (United Kingdom)","ror":"https://ror.org/0576dtf44","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210165610"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Simon Cross","raw_affiliation_strings":["Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5\r5NE, United Kingdom","Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5 5NE, United Kingdom. simon@moldiscovery.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5\r5NE, United Kingdom","institution_ids":["https://openalex.org/I4210165610"]},{"raw_affiliation_string":"Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5 5NE, United Kingdom. simon@moldiscovery.com","institution_ids":["https://openalex.org/I4210165610"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051485005","display_name":"Francesco Ortuso","orcid":"https://orcid.org/0000-0001-6235-8161"},"institutions":[{"id":"https://openalex.org/I36443711","display_name":"Magna Graecia University","ror":"https://ror.org/0530bdk91","country_code":"IT","type":"education","lineage":["https://openalex.org/I36443711"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Ortuso","raw_affiliation_strings":["Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy","institution_ids":["https://openalex.org/I36443711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083725137","display_name":"Massimo Baroni","orcid":"https://orcid.org/0000-0003-0866-148X"},"institutions":[{"id":"https://openalex.org/I4210165610","display_name":"Molecular Discovery (United Kingdom)","ror":"https://ror.org/0576dtf44","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210165610"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Massimo Baroni","raw_affiliation_strings":["Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5\r5NE, United Kingdom","Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5#R#5NE, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5\r5NE, United Kingdom","institution_ids":["https://openalex.org/I4210165610"]},{"raw_affiliation_string":"Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5#R#5NE, United Kingdom","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027151517","display_name":"Giosu\u00e8 Costa","orcid":"https://orcid.org/0000-0003-0947-9479"},"institutions":[{"id":"https://openalex.org/I36443711","display_name":"Magna Graecia University","ror":"https://ror.org/0530bdk91","country_code":"IT","type":"education","lineage":["https://openalex.org/I36443711"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giosu\u00e8 Costa","raw_affiliation_strings":["Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy","institution_ids":["https://openalex.org/I36443711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002260688","display_name":"Simona Distinto","orcid":"https://orcid.org/0000-0003-1620-6225"},"institutions":[{"id":"https://openalex.org/I36443711","display_name":"Magna Graecia University","ror":"https://ror.org/0530bdk91","country_code":"IT","type":"education","lineage":["https://openalex.org/I36443711"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simona Distinto","raw_affiliation_strings":["Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy","institution_ids":["https://openalex.org/I36443711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057095436","display_name":"Federica Moraca","orcid":"https://orcid.org/0000-0002-1077-1971"},"institutions":[{"id":"https://openalex.org/I36443711","display_name":"Magna Graecia University","ror":"https://ror.org/0530bdk91","country_code":"IT","type":"education","lineage":["https://openalex.org/I36443711"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Federica Moraca","raw_affiliation_strings":["Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy","institution_ids":["https://openalex.org/I36443711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022120195","display_name":"Stefano Alcaro","orcid":"https://orcid.org/0000-0002-0437-358X"},"institutions":[{"id":"https://openalex.org/I36443711","display_name":"Magna Graecia University","ror":"https://ror.org/0530bdk91","country_code":"IT","type":"education","lineage":["https://openalex.org/I36443711"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Alcaro","raw_affiliation_strings":["Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory\rof Computational\rMedicinal Chemistry, Department of \u201cScienze della Salute\u201d, University \u201cMagna Gr\u00e6cia\u201d of Catanzaro, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy","institution_ids":["https://openalex.org/I36443711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049965061","display_name":"Gabriele Cruciani","orcid":"https://orcid.org/0000-0002-4162-8692"},"institutions":[{"id":"https://openalex.org/I27483092","display_name":"University of Perugia","ror":"https://ror.org/00x27da85","country_code":"IT","type":"education","lineage":["https://openalex.org/I27483092"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriele Cruciani","raw_affiliation_strings":["Laboratory for Chemometrics and\rCheminformatics, Chemistry Department, University of Perugia, Via Elce di sotto 10, I-06123 Perugia, Italy","Laboratory for Chemometrics and#R#Cheminformatics, Chemistry Department, University of Perugia, Via Elce di sotto 10, I-06123 Perugia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Chemometrics and\rCheminformatics, Chemistry Department, University of Perugia, Via Elce di sotto 10, I-06123 Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]},{"raw_affiliation_string":"Laboratory for Chemometrics and#R#Cheminformatics, Chemistry Department, University of Perugia, Via Elce di sotto 10, I-06123 Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032652911"],"corresponding_institution_ids":["https://openalex.org/I4210165610"],"apc_list":null,"apc_paid":null,"fwci":7.1397,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.97514822,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"52","issue":"10","first_page":"2599","last_page":"2608"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9824000000953674,"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/pharmacophore","display_name":"Pharmacophore","score":0.9688854217529297},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.6630496382713318},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6617751717567444},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6470630764961243},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6162872314453125},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5599163770675659},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.5328327417373657},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5163282752037048},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2493690848350525},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2482832968235016},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.1447535753250122}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9688854217529297},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6630496382713318},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6617751717567444},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6470630764961243},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6162872314453125},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5599163770675659},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.5328327417373657},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5163282752037048},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2493690848350525},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2482832968235016},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.1447535753250122},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001688","descriptor_name":"Biological Products","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001688","descriptor_name":"Biological Products","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001688","descriptor_name":"Biological Products","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"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":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci300154n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300154n","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:22970854","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22970854","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:iris.unica.it:11584/90206","is_oa":false,"landing_page_url":"http://hdl.handle.net/11584/90206","pdf_url":null,"source":{"id":"https://openalex.org/S4377196293","display_name":"UNICA IRIS Institutional Research Information System (University of Cagliari)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172446870","host_organization_name":"University of Cagliari","host_organization_lineage":["https://openalex.org/I172446870"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320326073","display_name":"Regione Calabria","ror":null},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1491938055","https://openalex.org/W1968301816","https://openalex.org/W1973652931","https://openalex.org/W1995627555","https://openalex.org/W1995746750","https://openalex.org/W1995852445","https://openalex.org/W1996966884","https://openalex.org/W1999491936","https://openalex.org/W2007348965","https://openalex.org/W2039047003","https://openalex.org/W2039709045","https://openalex.org/W2058820833","https://openalex.org/W2070756053","https://openalex.org/W2080653934","https://openalex.org/W2111373893","https://openalex.org/W2127760066","https://openalex.org/W2152326664","https://openalex.org/W2166674455","https://openalex.org/W2204075485","https://openalex.org/W2208203352"],"related_works":["https://openalex.org/W42225299","https://openalex.org/W2943414817","https://openalex.org/W2197392606","https://openalex.org/W1605005150","https://openalex.org/W3184587995","https://openalex.org/W3092402433","https://openalex.org/W1482441085","https://openalex.org/W2966858528","https://openalex.org/W2151687600","https://openalex.org/W3114272811"],"abstract_inverted_index":{"To":[0],"date,":[1],"published":[2,140],"pharmacophore":[3,134,267],"elucidation":[4,135,268],"approaches":[5],"typically":[6],"use":[7],"a":[8,19,240,266],"handful":[9],"of":[10,114,145,152,178,194,200,207],"data":[11,20,86,119,154,197,231,270],"sets":[12],"for":[13,22,112,176,192],"validation:":[14],"here,":[15],"we":[16,83,259],"have":[17,127,260],"assembled":[18,45],"set":[21,87,155,232,271],"81":[23],"targets,":[24,33],"containing":[25],"960":[26],"ligands":[27,180],"aligned":[28],"using":[29],"their":[30,72],"cocrystallized":[31],"protein":[32],"to":[34,46,56,74,93,98,105,132,171,183,188,218,227,243,246,273],"provide":[35],"the":[36,63,68,77,96,100,103,115,122,142,150,153,173,179,189,195,201,205,223,255,277],"experimental":[37],"\"gold":[38],"standard\".":[39],"The":[40,229],"two-dimensional":[41,162],"structures":[42,59,163],"are":[43],"also":[44,182],"remove":[47],"conformational":[48],"bias;":[49],"an":[50],"ideal":[51],"method":[52,136],"would":[53],"be":[54,219,274],"able":[55,170],"take":[57],"these":[58],"as":[60],"input,":[61],"find":[62],"common":[64],"features,":[65],"and":[66,71,88,107,121,148,156,164,181],"reproduce":[67],"bioactive":[69,101,174],"conformations":[70,175],"alignments":[73,249],"correspond":[75],"with":[76,239],"X-ray-determined":[78],"gold":[79],"standard":[80],"alignments.":[81],"Here":[82],"present":[84],"this":[85,110,129,146,208],"describe":[89],"three":[90],"objective":[91,157],"measures":[92],"evaluate":[94],"performance:":[95],"ability":[97,104],"identify":[99,106,172],"conformation,":[102],"correctly":[108],"align":[109],"conformation":[111],"50%":[113],"molecules":[116],"in":[117,141,254],"each":[118],"set,":[120],"pharmacophoric":[123],"field":[124],"similarity.":[125],"We":[126],"applied":[128],"validation":[130],"methodology":[131],"our":[133],"FLAPpharm,":[137],"that":[138,258],"is":[139,233],"first":[143],"paper":[144],"series":[147],"discuss":[149],"limitations":[151],"success":[158,225],"criteria.":[159],"Starting":[160],"from":[161,251],"producing":[165],"unbiased":[166],"models,":[167],"FLAPpharm":[168],"was":[169],"67%":[177,193],"produce":[184],"successful":[185],"models":[186,203],"according":[187],"second":[190],"metric":[191],"Pharmbench":[196],"sets.":[198],"Inspection":[199],"unsuccessful":[202],"highlighted":[204],"limitation":[206],"root":[209],"mean":[210],"square":[211],"(rms)-derived":[212],"metric,":[213],"since":[214],"many":[215],"were":[216],"found":[217],"pharmacophorically":[220],"reasonable,":[221],"increasing":[222],"overall":[224],"rate":[226],"83%.":[228],"PharmBench":[230],"available":[234,272],"at":[235],"http://www.moldiscovery.com/PharmBench":[236],",":[237],"along":[238],"web":[241],"service":[242],"enable":[244],"users":[245],"score":[247],"model":[248],"coming":[250],"external":[252],"methods":[253],"same":[256],"way":[257],"presented":[261],"here":[262],"and,":[263],"therefore,":[264],"establishes":[265],"benchmark":[269],"used":[275],"by":[276],"community.":[278]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
