{"id":"https://openalex.org/W2066396351","doi":"https://doi.org/10.1021/ci200626m","title":"Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA.","display_name":"Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA.","publication_year":2012,"publication_date":"2012-05-31","ids":{"openalex":"https://openalex.org/W2066396351","doi":"https://doi.org/10.1021/ci200626m","mag":"2066396351","pmid":"https://pubmed.ncbi.nlm.nih.gov/22651699"},"language":"en","primary_location":{"id":"doi:10.1021/ci200626m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200626m","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/A5057817284","display_name":"Maria Safi","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Maria Safi","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada","Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada#TAB#","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071031693","display_name":"Ryan Lilien","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ryan H. Lilien","raw_affiliation_strings":["Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada","Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada#TAB#","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5057817284"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":null,"apc_paid":null,"fwci":0.6262,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.66898943,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"52","issue":"6","first_page":"1529","last_page":"1541"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9941999912261963,"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/T11845","display_name":"Cancer therapeutics and mechanisms","score":0.9933000206947327,"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/dihydrofolate-reductase","display_name":"Dihydrofolate reductase","score":0.73403000831604},{"id":"https://openalex.org/keywords/drug-resistance","display_name":"Drug resistance","score":0.6714286804199219},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5076509714126587},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.487870454788208},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.45637381076812744},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38034170866012573},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.3514127731323242},{"id":"https://openalex.org/keywords/methotrexate","display_name":"Methotrexate","score":0.2288890779018402},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21851509809494019},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2175731658935547},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.09377238154411316}],"concepts":[{"id":"https://openalex.org/C2781320022","wikidata":"https://www.wikidata.org/wiki/Q417149","display_name":"Dihydrofolate reductase","level":3,"score":0.73403000831604},{"id":"https://openalex.org/C114851261","wikidata":"https://www.wikidata.org/wiki/Q12147416","display_name":"Drug resistance","level":2,"score":0.6714286804199219},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5076509714126587},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.487870454788208},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.45637381076812744},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38034170866012573},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.3514127731323242},{"id":"https://openalex.org/C2781059491","wikidata":"https://www.wikidata.org/wiki/Q422232","display_name":"Methotrexate","level":2,"score":0.2288890779018402},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21851509809494019},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2175731658935547},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.09377238154411316}],"mesh":[{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000998","descriptor_name":"Antiviral Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000998","descriptor_name":"Antiviral Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000998","descriptor_name":"Antiviral Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200626m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200626m","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:22651699","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22651699","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":[{"score":0.8600000143051147,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":70,"referenced_works":["https://openalex.org/W141181845","https://openalex.org/W1494686030","https://openalex.org/W1527359370","https://openalex.org/W1965205049","https://openalex.org/W1970131292","https://openalex.org/W1970250279","https://openalex.org/W1970503235","https://openalex.org/W1972728295","https://openalex.org/W1974647057","https://openalex.org/W1974884195","https://openalex.org/W1977899779","https://openalex.org/W1979046104","https://openalex.org/W1986124907","https://openalex.org/W1992355680","https://openalex.org/W1995807192","https://openalex.org/W1997107638","https://openalex.org/W2009529127","https://openalex.org/W2012238745","https://openalex.org/W2012490272","https://openalex.org/W2016238865","https://openalex.org/W2016380176","https://openalex.org/W2017506441","https://openalex.org/W2017604095","https://openalex.org/W2025156367","https://openalex.org/W2035910652","https://openalex.org/W2036571761","https://openalex.org/W2042112674","https://openalex.org/W2043560498","https://openalex.org/W2047266495","https://openalex.org/W2047558831","https://openalex.org/W2048644502","https://openalex.org/W2048986518","https://openalex.org/W2053462619","https://openalex.org/W2058895505","https://openalex.org/W2072287929","https://openalex.org/W2073125464","https://openalex.org/W2083657154","https://openalex.org/W2087487987","https://openalex.org/W2089961932","https://openalex.org/W2093381148","https://openalex.org/W2096453179","https://openalex.org/W2097732752","https://openalex.org/W2103631613","https://openalex.org/W2104015266","https://openalex.org/W2113264508","https://openalex.org/W2114764466","https://openalex.org/W2116121986","https://openalex.org/W2117767830","https://openalex.org/W2118233996","https://openalex.org/W2119249830","https://openalex.org/W2122199548","https://openalex.org/W2124002599","https://openalex.org/W2127458207","https://openalex.org/W2128034051","https://openalex.org/W2131619400","https://openalex.org/W2134463729","https://openalex.org/W2135890487","https://openalex.org/W2136065656","https://openalex.org/W2138072853","https://openalex.org/W2140227530","https://openalex.org/W2142868265","https://openalex.org/W2143537616","https://openalex.org/W2150155770","https://openalex.org/W2150215096","https://openalex.org/W2154348803","https://openalex.org/W2166136759","https://openalex.org/W2169790816","https://openalex.org/W2179482622","https://openalex.org/W2200703846","https://openalex.org/W4297914773"],"related_works":["https://openalex.org/W2063930242","https://openalex.org/W2147932467","https://openalex.org/W2593258460","https://openalex.org/W2218040621","https://openalex.org/W2013003323","https://openalex.org/W2086452998","https://openalex.org/W1981076832","https://openalex.org/W2024773645","https://openalex.org/W2001717001","https://openalex.org/W2043147644"],"abstract_inverted_index":{"Active":[0],"site":[1],"mutations":[2,72,119],"that":[3,57,73],"disrupt":[4],"drug":[5,12,33,47,75],"binding":[6,76],"are":[7,22],"an":[8,43],"important":[9],"mechanism":[10],"of":[11,17,32,52,62,134],"resistance.":[13,63],"Computational":[14],"methods":[15],"capable":[16],"predicting":[18,46],"resistance":[19,48,90,118,136],"a":[20,67],"priori":[21],"poised":[23],"to":[24,45,70,88],"become":[25],"extremely":[26],"useful":[27],"tools":[28],"in":[29,91],"the":[30,50,81,128,132],"fields":[31],"discovery":[34],"and":[35,55,105,107],"treatment":[36],"design.":[37],"In":[38,125],"this":[39],"paper,":[40],"we":[41],"describe":[42],"approach":[44],"on":[49],"basis":[51],"Dead-End":[53],"Elimination":[54],"MM-PBSA":[56],"requires":[58],"no":[59],"prior":[60],"knowledge":[61],"Our":[64],"method":[65,87],"utilizes":[66],"two-pass":[68],"search":[69],"identify":[71],"impair":[74],"while":[77],"maintaining":[78],"affinity":[79],"for":[80,120],"native":[82],"substrate.":[83],"We":[84,111],"use":[85],"our":[86,113],"probe":[89],"four":[92,122],"drug-target":[93],"systems:":[94],"isoniazid-enoyl-ACP":[95],"reductase":[96,102],"(tuberculosis),":[97],"ritonavir-HIV":[98],"protease":[99],"(HIV),":[100],"methotrexate-dihydrofolate":[101],"(breast":[103],"cancer":[104],"leukemia),":[106],"gleevec-ABL":[108],"kinase":[109],"(leukemia).":[110],"validate":[112],"model":[114,129],"using":[115],"clinically":[116],"known":[117,135],"all":[121,126],"test":[123],"systems.":[124],"cases,":[127],"correctly":[130],"predicts":[131],"majority":[133],"mutations.":[137]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
