{"id":"https://openalex.org/W2091060157","doi":"https://doi.org/10.1021/ci900074t","title":"Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4","display_name":"Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4","publication_year":2010,"publication_date":"2010-01-07","ids":{"openalex":"https://openalex.org/W2091060157","doi":"https://doi.org/10.1021/ci900074t","mag":"2091060157","pmid":"https://pubmed.ncbi.nlm.nih.gov/20055489"},"language":"en","primary_location":{"id":"doi:10.1021/ci900074t","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900074t","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":"http://pubs.acs.org/doi/abs/10.1021/ci900074t","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021322465","display_name":"Renato Ferreira de Freitas","orcid":"https://orcid.org/0000-0001-6195-4236"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"R. F. Freitas","raw_affiliation_strings":["Grupo de Estudos em Qu\u00edmica Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Qu\u00edmica de S\u00e3o Carlos - Universidade de S\u00e3o Paulo, 13560-970 - S\u00e3o Carlos - SP, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grupo de Estudos em Qu\u00edmica Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Qu\u00edmica de S\u00e3o Carlos - Universidade de S\u00e3o Paulo, 13560-970 - S\u00e3o Carlos - SP, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098118916","display_name":"R. L. Bauab","orcid":null},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"R. L. Bauab","raw_affiliation_strings":["Grupo de Estudos em Qu\u00edmica Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Qu\u00edmica de S\u00e3o Carlos - Universidade de S\u00e3o Paulo, 13560-970 - S\u00e3o Carlos - SP, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grupo de Estudos em Qu\u00edmica Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Qu\u00edmica de S\u00e3o Carlos - Universidade de S\u00e3o Paulo, 13560-970 - S\u00e3o Carlos - SP, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039642161","display_name":"Carlos A. Montanari","orcid":"https://orcid.org/0000-0002-4963-0316"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"C. A. Montanari","raw_affiliation_strings":["Grupo de Estudos em Qu\u00edmica Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Qu\u00edmica de S\u00e3o Carlos - Universidade de S\u00e3o Paulo, 13560-970 - S\u00e3o Carlos - SP, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grupo de Estudos em Qu\u00edmica Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Qu\u00edmica de S\u00e3o Carlos - Universidade de S\u00e3o Paulo, 13560-970 - S\u00e3o Carlos - SP, Brazil","institution_ids":["https://openalex.org/I17974374"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5039642161"],"corresponding_institution_ids":["https://openalex.org/I17974374"],"apc_list":null,"apc_paid":null,"fwci":3.0445,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.91389121,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"50","issue":"1","first_page":"97","last_page":"109"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"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":0.9993000030517578,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9836999773979187,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5956030488014221},{"id":"https://openalex.org/keywords/cyp2c9","display_name":"CYP2C9","score":0.4520851671695709},{"id":"https://openalex.org/keywords/cytochrome-p450","display_name":"Cytochrome P450","score":0.44070008397102356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4147476851940155},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36948728561401367},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33879372477531433},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2672101855278015},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2110356092453003},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.183185875415802},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.11691299080848694}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5956030488014221},{"id":"https://openalex.org/C3946865","wikidata":"https://www.wikidata.org/wiki/Q5014962","display_name":"CYP2C9","level":4,"score":0.4520851671695709},{"id":"https://openalex.org/C526171541","wikidata":"https://www.wikidata.org/wiki/Q407693","display_name":"Cytochrome P450","level":3,"score":0.44070008397102356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4147476851940155},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36948728561401367},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33879372477531433},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2672101855278015},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2110356092453003},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.183185875415802},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.11691299080848694},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003577","descriptor_name":"Cytochrome P-450 Enzyme System","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003577","descriptor_name":"Cytochrome P-450 Enzyme System","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003577","descriptor_name":"Cytochrome P-450 Enzyme System","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007527","descriptor_name":"Isoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007527","descriptor_name":"Isoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007527","descriptor_name":"Isoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D011485","descriptor_name":"Protein Binding","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":"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":"D019389","descriptor_name":"Cytochrome P-450 CYP2D6","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019389","descriptor_name":"Cytochrome P-450 CYP2D6","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019389","descriptor_name":"Cytochrome P-450 CYP2D6","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051544","descriptor_name":"Cytochrome P-450 CYP3A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051544","descriptor_name":"Cytochrome P-450 CYP3A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051544","descriptor_name":"Cytochrome P-450 CYP3A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/ci900074t","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900074t","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:20055489","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20055489","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:001810538","is_oa":true,"landing_page_url":"http://pubs.acs.org/doi/abs/10.1021/ci900074t","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"instacron:USP","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:www.producao.usp.br:BDPI/31887","is_oa":false,"landing_page_url":"http://producao.usp.br/handle/BDPI/31887","pdf_url":null,"source":{"id":"https://openalex.org/S4306401373","display_name":"Scientific Electronic Library Online (S\u00e3o Paulo Research Foundation, Latin American and Caribbean Center on Health Sciences Information, Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2982035970","host_organization_name":"Costa Rican Department of Social Security","host_organization_lineage":["https://openalex.org/I2982035970"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"article"}],"best_oa_location":{"id":"pmh:001810538","is_oa":true,"landing_page_url":"http://pubs.acs.org/doi/abs/10.1021/ci900074t","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"instacron:USP","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6399999856948853}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W639366881","https://openalex.org/W1572125866","https://openalex.org/W1832059623","https://openalex.org/W1968127936","https://openalex.org/W1979597166","https://openalex.org/W1982996392","https://openalex.org/W1990451437","https://openalex.org/W1992475241","https://openalex.org/W1997039157","https://openalex.org/W2000541041","https://openalex.org/W2002755329","https://openalex.org/W2015907087","https://openalex.org/W2017314173","https://openalex.org/W2040324575","https://openalex.org/W2042110087","https://openalex.org/W2042624251","https://openalex.org/W2058433776","https://openalex.org/W2062145093","https://openalex.org/W2074402745","https://openalex.org/W2080156380","https://openalex.org/W2097100227","https://openalex.org/W2101900366","https://openalex.org/W2119126379","https://openalex.org/W2123275178","https://openalex.org/W2125253492","https://openalex.org/W2125792789","https://openalex.org/W2132349145","https://openalex.org/W2144724079","https://openalex.org/W2147761750","https://openalex.org/W2150496339","https://openalex.org/W2159822007"],"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/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W2040113886","https://openalex.org/W2580961670"],"abstract_inverted_index":{"Cytochrome":[0],"P450":[1],"(CYP450)":[2],"is":[3,12],"a":[4,94,132,151,165],"class":[5],"of":[6,43,59,71,74,88,106,118,150,164],"enzymes":[7,63],"where":[8],"the":[9,41,44,69,72,86,121,137,143,148,162],"substrate":[10],"identification":[11],"particularly":[13],"important":[14,61],"to":[15,22,30,34,56],"know.":[16],"It":[17],"would":[18],"help":[19],"medicinal":[20],"chemists":[21],"design":[23],"drugs":[24],"with":[25,53,114],"lower":[26],"side":[27],"effects":[28],"due":[29],"drug-drug":[31],"interactions":[32],"and":[33,46,66,109,136],"extensive":[35],"genetic":[36],"polymorphism.":[37],"Herein,":[38],"we":[39,84],"discuss":[40],"application":[42],"2D":[45],"3D-similarity":[47],"searches":[48,127],"in":[49],"identifying":[50],"reference":[51,76],"structures":[52,77],"higher":[54],"capacity":[55],"retrieve":[57],"substrates":[58,158],"three":[60],"CYP":[62],"(CYP2C9,":[64],"CYP2D6,":[65],"CYP3A4).":[67],"On":[68],"basis":[70],"complementarities":[73],"multiple":[75],"selected":[78],"by":[79,141],"different":[80],"similarity":[81,126],"search":[82],"methods,":[83],"proposed":[85],"fusion":[87],"their":[89],"individual":[90],"Tanimoto":[91,96],"scores":[92],"into":[93],"consensus":[95],"score":[97],"(T(consensus)).":[98],"Using":[99],"this":[100],"new":[101],"score,":[102,145],"true":[103],"positive":[104,116],"rates":[105,117],"63%":[107],"(CYP2C9)":[108],"81%":[110],"(CYP2D6)":[111],"were":[112,128,159],"achieved":[113],"false":[115],"4%":[119],"for":[120],"CYP2C9-CYP2D6":[122],"data":[123,134],"set.":[124],"Extended":[125],"carried":[129],"out":[130],"on":[131],"validation":[133],"set,":[135],"results":[138],"showed":[139],"that":[140],"using":[142],"T(consensus)":[144],"not":[146],"only":[147],"area":[149],"ROC":[152],"graph":[153],"increased,":[154],"but":[155],"also":[156],"more":[157],"recovered":[160],"at":[161],"beginning":[163],"ranked":[166],"list.":[167]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
