{"id":"https://openalex.org/W2054136576","doi":"https://doi.org/10.1021/ci400058s","title":"Prediction of Cytochrome P450 Xenobiotic Metabolism: Tethered Docking and Reactivity Derived from Ligand Molecular Orbital Analysis","display_name":"Prediction of Cytochrome P450 Xenobiotic Metabolism: Tethered Docking and Reactivity Derived from Ligand Molecular Orbital Analysis","publication_year":2013,"publication_date":"2013-05-24","ids":{"openalex":"https://openalex.org/W2054136576","doi":"https://doi.org/10.1021/ci400058s","mag":"2054136576","pmid":"https://pubmed.ncbi.nlm.nih.gov/23701380"},"language":"en","primary_location":{"id":"doi:10.1021/ci400058s","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400058s","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/A5078919568","display_name":"Jonathan D. Tyzack","orcid":"https://orcid.org/0000-0003-4827-9023"},"institutions":[{"id":"https://openalex.org/I1342131907","display_name":"Unilever (United Kingdom)","ror":"https://ror.org/05n8ah907","country_code":"GB","type":"company","lineage":["https://openalex.org/I1342131907"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jonathan D. Tyzack","raw_affiliation_strings":["Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom","institution_ids":["https://openalex.org/I1342131907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073259642","display_name":"Mark J. Williamson","orcid":"https://orcid.org/0000-0002-5295-7811"},"institutions":[{"id":"https://openalex.org/I1342131907","display_name":"Unilever (United Kingdom)","ror":"https://ror.org/05n8ah907","country_code":"GB","type":"company","lineage":["https://openalex.org/I1342131907"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark J. Williamson","raw_affiliation_strings":["Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom","institution_ids":["https://openalex.org/I1342131907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002165980","display_name":"Rubben Torella","orcid":"https://orcid.org/0000-0003-0765-2098"},"institutions":[{"id":"https://openalex.org/I1342131907","display_name":"Unilever (United Kingdom)","ror":"https://ror.org/05n8ah907","country_code":"GB","type":"company","lineage":["https://openalex.org/I1342131907"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rubben Torella","raw_affiliation_strings":["Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom","institution_ids":["https://openalex.org/I1342131907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014283781","display_name":"Robert C. Glen","orcid":"https://orcid.org/0000-0003-1759-2914"},"institutions":[{"id":"https://openalex.org/I1342131907","display_name":"Unilever (United Kingdom)","ror":"https://ror.org/05n8ah907","country_code":"GB","type":"company","lineage":["https://openalex.org/I1342131907"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Robert C. Glen","raw_affiliation_strings":["Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom","institution_ids":["https://openalex.org/I1342131907"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5014283781"],"corresponding_institution_ids":["https://openalex.org/I1342131907"],"apc_list":null,"apc_paid":null,"fwci":8.7485,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.98233469,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"53","issue":"6","first_page":"1294","last_page":"1305"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9991999864578247,"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":0.9983999729156494,"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/docking","display_name":"Docking (animal)","score":0.72243332862854},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6291489005088806},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5699557065963745},{"id":"https://openalex.org/keywords/cytochrome-p450","display_name":"Cytochrome P450","score":0.5661543607711792},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5108470320701599},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4753130078315735},{"id":"https://openalex.org/keywords/xenobiotic","display_name":"Xenobiotic","score":0.45711448788642883},{"id":"https://openalex.org/keywords/drug-metabolism","display_name":"Drug metabolism","score":0.45490723848342896},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.42986056208610535},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4279179573059082},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4165421426296234},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.35834604501724243},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.17992675304412842},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1734207570552826},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.12472930550575256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09783792495727539},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.07929617166519165}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.72243332862854},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6291489005088806},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5699557065963745},{"id":"https://openalex.org/C526171541","wikidata":"https://www.wikidata.org/wiki/Q407693","display_name":"Cytochrome P450","level":3,"score":0.5661543607711792},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5108470320701599},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4753130078315735},{"id":"https://openalex.org/C115448650","wikidata":"https://www.wikidata.org/wiki/Q409205","display_name":"Xenobiotic","level":3,"score":0.45711448788642883},{"id":"https://openalex.org/C89311334","wikidata":"https://www.wikidata.org/wiki/Q1124842","display_name":"Drug metabolism","level":3,"score":0.45490723848342896},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.42986056208610535},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4279179573059082},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4165421426296234},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.35834604501724243},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.17992675304412842},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1734207570552826},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.12472930550575256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09783792495727539},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.07929617166519165},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015262","descriptor_name":"Xenobiotics","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015262","descriptor_name":"Xenobiotics","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015262","descriptor_name":"Xenobiotics","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci400058s","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400058s","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:23701380","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23701380","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":82,"referenced_works":["https://openalex.org/W1565260601","https://openalex.org/W1965092590","https://openalex.org/W1968400590","https://openalex.org/W1971223189","https://openalex.org/W1972127956","https://openalex.org/W1973057639","https://openalex.org/W1973191530","https://openalex.org/W1974254541","https://openalex.org/W1976499671","https://openalex.org/W1982320452","https://openalex.org/W1982439290","https://openalex.org/W1984465513","https://openalex.org/W1984648567","https://openalex.org/W1985588649","https://openalex.org/W1989555601","https://openalex.org/W1995106631","https://openalex.org/W2000872531","https://openalex.org/W2001330182","https://openalex.org/W2002638182","https://openalex.org/W2009069469","https://openalex.org/W2009458392","https://openalex.org/W2014919794","https://openalex.org/W2020040806","https://openalex.org/W2023271753","https://openalex.org/W2024469207","https://openalex.org/W2024897249","https://openalex.org/W2025317111","https://openalex.org/W2025417017","https://openalex.org/W2027549508","https://openalex.org/W2029667189","https://openalex.org/W2031655565","https://openalex.org/W2032615225","https://openalex.org/W2035266068","https://openalex.org/W2039781258","https://openalex.org/W2043554648","https://openalex.org/W2045733364","https://openalex.org/W2049557754","https://openalex.org/W2051300664","https://openalex.org/W2051682290","https://openalex.org/W2052958668","https://openalex.org/W2055031731","https://openalex.org/W2060943223","https://openalex.org/W2062382607","https://openalex.org/W2063083610","https://openalex.org/W2065895273","https://openalex.org/W2067174909","https://openalex.org/W2079202542","https://openalex.org/W2082438252","https://openalex.org/W2083469020","https://openalex.org/W2089887872","https://openalex.org/W2090505208","https://openalex.org/W2095533951","https://openalex.org/W2104925243","https://openalex.org/W2105587896","https://openalex.org/W2105668062","https://openalex.org/W2106050611","https://openalex.org/W2106140689","https://openalex.org/W2107423623","https://openalex.org/W2109402847","https://openalex.org/W2113149246","https://openalex.org/W2114520383","https://openalex.org/W2115644937","https://openalex.org/W2117000356","https://openalex.org/W2123969193","https://openalex.org/W2124137657","https://openalex.org/W2126901834","https://openalex.org/W2130479394","https://openalex.org/W2130983257","https://openalex.org/W2138972881","https://openalex.org/W2144288821","https://openalex.org/W2150928826","https://openalex.org/W2153467586","https://openalex.org/W2154598050","https://openalex.org/W2161069015","https://openalex.org/W2164071972","https://openalex.org/W2165043147","https://openalex.org/W2165565773","https://openalex.org/W2165779834","https://openalex.org/W2169678694","https://openalex.org/W2215622966","https://openalex.org/W4233234749","https://openalex.org/W4236010144"],"related_works":["https://openalex.org/W3021897254","https://openalex.org/W4387808345","https://openalex.org/W3006796381","https://openalex.org/W3021656239","https://openalex.org/W4376472519","https://openalex.org/W143672087","https://openalex.org/W2133881279","https://openalex.org/W2040874707","https://openalex.org/W1559593361","https://openalex.org/W2360905569"],"abstract_inverted_index":{"Metabolism":[0],"of":[1,18,20,34,74,89,108,123,127,130,157,177,221],"xenobiotic":[2],"and":[3,12,111,137,155,183,191,201,219,228,235],"endogenous":[4],"compounds":[5],"is":[6,54,84,144,163,171],"frequently":[7],"complex,":[8],"not":[9],"completely":[10],"elucidated,":[11],"therefore":[13],"often":[14],"ambiguous.":[15],"The":[16],"prediction":[17,241],"sites":[19],"metabolism":[21],"(SoM)":[22],"can":[23],"be":[24,209],"particularly":[25],"helpful":[26],"as":[27],"a":[28,36,46,71,105,117,167,206],"first":[29,125],"step":[30],"toward":[31],"the":[32,58,75,87,90,124,148,175,189,212,222],"identification":[33],"metabolites,":[35],"process":[37],"especially":[38],"relevant":[39],"to":[40,95,113,208],"drug":[41],"discovery.":[42],"This":[43],"paper":[44],"describes":[45],"reactivity":[47,53,192],"approach":[48,170],"for":[49,104,216,225],"predicting":[50],"SoM":[51,83,207],"whereby":[52],"derived":[55],"directly":[56],"from":[57,147,198],"ground":[59],"state":[60,143],"ligand":[61,184],"molecular":[62,109,128],"orbital":[63],"analysis,":[64],"calculated":[65,103],"using":[66,70,161,185,195],"Density":[67],"Functional":[68],"Theory,":[69],"novel":[72],"implementation":[73],"average":[76],"local":[77],"ionization":[78],"energy.":[79],"Thus":[80],"each":[81],"potential":[82],"sampled":[85],"in":[86,93,116,139,211],"context":[88],"whole":[91],"ligand,":[92],"contrast":[94],"other":[96,238],"popular":[97],"approaches":[98,160],"where":[99],"activation":[100],"energies":[101],"are":[102,233],"predefined":[106],"database":[107],"fragments":[110],"assigned":[112],"matching":[114],"moieties":[115],"query":[118],"ligand.":[119],"In":[120,165],"addition,":[121],"one":[122],"descriptions":[126],"dynamics":[129],"cytochrome":[131],"P450":[132],"(CYP)":[133],"isoforms":[134],"3A4,":[135,226],"2D6,":[136,227],"2C9":[138],"their":[140],"Compound":[141],"I":[142],"reported,":[145],"and,":[146],"representative":[149],"protein":[150],"structures":[151],"obtained,":[152],"an":[153],"analysis":[154],"evaluation":[156],"various":[158],"docking":[159,169,190,200],"GOLD":[162],"performed.":[164],"particular,":[166],"covalent":[168],"described":[172],"coupled":[173],"with":[174,237],"modeling":[176],"important":[178],"electrostatic":[179],"interactions":[180],"between":[181],"CYP":[182],"spherical":[186],"constraints.":[187],"Combining":[188],"results,":[193],"obtained":[194],"standard":[196],"functionality":[197],"common":[199],"quantum":[202],"chemical":[203],"applications,":[204],"enables":[205],"identified":[210],"top":[213],"2":[214],"predictions":[215],"75%,":[217],"80%,":[218],"78%":[220],"data":[223],"sets":[224],"2C9,":[229],"respectively,":[230],"results":[231],"that":[232],"accessible":[234],"competitive":[236],"recently":[239],"published":[240],"tools.":[242]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
