{"id":"https://openalex.org/W1993526458","doi":"https://doi.org/10.1021/ci200234p","title":"Development of a Minimal Kinase Ensemble Receptor (MKER) for Surrogate AutoShim","display_name":"Development of a Minimal Kinase Ensemble Receptor (MKER) for Surrogate AutoShim","publication_year":2011,"publication_date":"2011-08-17","ids":{"openalex":"https://openalex.org/W1993526458","doi":"https://doi.org/10.1021/ci200234p","mag":"1993526458","pmid":"https://pubmed.ncbi.nlm.nih.gov/21848284"},"language":"en","primary_location":{"id":"doi:10.1021/ci200234p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200234p","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/A5013190334","display_name":"Prasenjit Mukherjee","orcid":"https://orcid.org/0000-0003-2424-0634"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Prasenjit Mukherjee","raw_affiliation_strings":["Oncology and Exploratory Chemistry, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oncology and Exploratory Chemistry, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080967157","display_name":"\u00c9ric Martin","orcid":"https://orcid.org/0000-0001-7040-5108"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eric Martin","raw_affiliation_strings":["Oncology and Exploratory Chemistry, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oncology and Exploratory Chemistry, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5013190334"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.07467113,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"51","issue":"10","first_page":"2697","last_page":"2705"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11736","display_name":"Histone Deacetylase Inhibitors Research","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9916999936103821,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37340623140335083},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.354861319065094},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32552391290664673},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24478590488433838}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37340623140335083},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.354861319065094},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32552391290664673},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24478590488433838}],"mesh":[{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200234p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200234p","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:21848284","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21848284","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1531401772","https://openalex.org/W1606544556","https://openalex.org/W1963681467","https://openalex.org/W1981429394","https://openalex.org/W2014915963","https://openalex.org/W2017337590","https://openalex.org/W2026535637","https://openalex.org/W2037452557","https://openalex.org/W2041701367","https://openalex.org/W2050456292","https://openalex.org/W2071447504","https://openalex.org/W2072026441","https://openalex.org/W2091823093","https://openalex.org/W2107835995","https://openalex.org/W2120216197","https://openalex.org/W2148633389","https://openalex.org/W2158534713","https://openalex.org/W2197112043","https://openalex.org/W3023540311"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"The":[0,59,175],"target-tailored":[1],"3-D":[2],"virtual":[3,193],"screening":[4],"(VS)":[5],"method":[6,109],"\"Surrogate":[7],"AutoShim\"":[8],"adds":[9],"pharmacophoric":[10],"shims":[11],"to":[12,22,65,120,171],"a":[13,30,123,133,149,213],"16-kinase":[14],"crystal":[15],"structure":[16],"\"Universal":[17],"Kinase":[18,135,204],"Ensemble":[19,136,205],"Receptor\"":[20,137],"(UKER)":[21],"generate":[23],"highly":[24],"predictive,":[25],"target-customized":[26],"docking":[27,53],"models.":[28,147],"Predocking":[29],"corporate":[31],"archive":[32],"of":[33,35,73,91,96,129,152,159,185,216],"millions":[34,90],"compounds":[36,93,165],"into":[37],"the":[38,45,51,103,108,130,141,172,179],"16-structure":[39],"ensemble":[40],"takes":[41,98],"months.":[42],"However,":[43],"since":[44],"16":[46,131],"UKER":[47],"structures":[48],"are":[49,62],"always":[50],"same,":[52],"need":[54],"only":[55,99,127,212],"be":[56],"done":[57],"once.":[58],"predocked":[60,92],"results":[61],"then":[63],"\"shimmed\"":[64],"reproduce":[66],"experimental":[67],"training":[68],"data":[69],"for":[70,89,144,181],"any":[71],"number":[72],"additional":[74],"kinases":[75,97],"far":[76],"more":[77,111],"accurately":[78],"than":[79],"conventional":[80],"docking.":[81],"Training":[82],"new":[83],"kinase":[84,146,161],"models":[85],"and":[86,163,187],"predicting":[87],"activity":[88],"against":[94],"dozens":[95],"hours.":[100],"However":[101],"reducing":[102],"predocking":[104,182,196],"time":[105,180],"would":[106],"make":[107],"even":[110],"advantageous.":[112],"Sequential":[113],"Floating":[114],"Forward":[115],"Search":[116],"(SFFS)":[117],"was":[118],"employed":[119],"rationally":[121],"identify":[122],"reduced":[124],"subset":[125,154],"using":[126],"8":[128],"structures,":[132],"\"Minimal":[134],"(MKER)":[138],"that":[139],"preserved":[140],"predictive":[142],"accuracy":[143],"20":[145],"Furthermore,":[148],"performance":[150,169],"evaluation":[151],"this":[153],"on":[155],"an":[156],"extended":[157],"set":[158],"52":[160],"targets":[162],"100,000":[164],"showed":[166],"statistical":[167],"model":[168],"comparable":[170],"original":[173],"UKER.":[174],"MKER":[176],"has":[177],"halved":[178],"large":[183],"databases":[184],"internal":[186],"commercial":[188],"compounds.":[189],"For":[190],"ad":[191],"hoc":[192],"libraries,":[194],"where":[195],"is":[197],"not":[198],"possible,":[199],"2-":[200],"or":[201],"3-kinases":[202],"\"Approximate":[203],"Receptors\"":[206],"(AKER)":[207],"were":[208],"also":[209],"identified":[210],"with":[211],"modest":[214],"loss":[215],"prediction":[217],"accuracy.":[218]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
