{"id":"https://openalex.org/W2461470610","doi":"https://doi.org/10.1021/acs.jcim.6b00290","title":"Computational Modeling of \u03b2-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches","display_name":"Computational Modeling of \u03b2-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches","publication_year":2016,"publication_date":"2016-09-30","ids":{"openalex":"https://openalex.org/W2461470610","doi":"https://doi.org/10.1021/acs.jcim.6b00290","mag":"2461470610","pmid":"https://pubmed.ncbi.nlm.nih.gov/27689393"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00290","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":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-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/A5009477614","display_name":"Govindan Subramanian","orcid":"https://orcid.org/0000-0002-6040-0415"},"institutions":[{"id":"https://openalex.org/I276601970","display_name":"Zoetis (United States)","ror":"https://ror.org/03k2dnh74","country_code":"US","type":"company","lineage":["https://openalex.org/I276601970"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Govindan Subramanian","raw_affiliation_strings":["VMRD\rGlobal Discovery, Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States"],"affiliations":[{"raw_affiliation_string":"VMRD\rGlobal Discovery, Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States","institution_ids":["https://openalex.org/I276601970"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039641760","display_name":"Bharath Ramsundar","orcid":"https://orcid.org/0000-0001-8450-4262"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bharath Ramsundar","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032418986","display_name":"Vijay S. Pande","orcid":"https://orcid.org/0000-0003-2774-1178"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vijay Pande","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5008338348","display_name":"R. Aldrin Denny","orcid":"https://orcid.org/0000-0001-7441-7077"},"institutions":[{"id":"https://openalex.org/I180857899","display_name":"Pfizer (United States)","ror":"https://ror.org/01xdqrp08","country_code":"US","type":"company","lineage":["https://openalex.org/I180857899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajiah Aldrin Denny","raw_affiliation_strings":["Worldwide\rMedicinal Chemistry, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States"],"affiliations":[{"raw_affiliation_string":"Worldwide\rMedicinal Chemistry, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States","institution_ids":["https://openalex.org/I180857899"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":9.616,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":211,"citation_normalized_percentile":{"value":0.938443,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"56","issue":"10","first_page":"1936","last_page":"1949"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Methods in Drug Discovery","score":0.9999,"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 Methods in Drug Discovery","score":0.9999,"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/T11882","display_name":"Biosynthesis and Engineering of Terpenoids","score":0.9853,"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/T10044","display_name":"Protein Structure Prediction and Analysis","score":0.982,"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/chemical-space","display_name":"Chemical space","score":0.6666136},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.5631497},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.5211825},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology Modeling","score":0.517106},{"id":"https://openalex.org/keywords/drug-target-identification","display_name":"Drug Target Identification","score":0.505338},{"id":"https://openalex.org/keywords/binary-classification","display_name":"Binary classification","score":0.41762424}],"concepts":[{"id":"https://openalex.org/C164126121","wikidata":"https://www.wikidata.org/wiki/Q766383","display_name":"Quantitative structure\u2013activity relationship","level":2,"score":0.6773006},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.6666136},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.65540016},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5922786},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.5631497},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.5211825},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5133804},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.50357693},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4936248},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.45969737},{"id":"https://openalex.org/C66905080","wikidata":"https://www.wikidata.org/wiki/Q17005494","display_name":"Binary classification","level":3,"score":0.41762424},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37725744},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3571328},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3569001},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.32873353},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.18490979},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08484769},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D053829","descriptor_name":"Amyloid Precursor Protein Secretases","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D016282","descriptor_name":"Aspartic Acid Endopeptidases","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053829","descriptor_name":"Amyloid Precursor Protein Secretases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D053829","descriptor_name":"Amyloid Precursor Protein Secretases","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053829","descriptor_name":"Amyloid Precursor Protein Secretases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016282","descriptor_name":"Aspartic Acid Endopeptidases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016282","descriptor_name":"Aspartic Acid Endopeptidases","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016282","descriptor_name":"Aspartic Acid Endopeptidases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00290","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":null,"is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27689393","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Peace, justice, and strong institutions","score":0.65,"id":"https://metadata.un.org/sdg/16"}],"grants":[{"funder":"https://openalex.org/F4320308782","funder_display_name":"Hertz Foundation","award_id":null}],"datasets":[],"versions":[],"referenced_works_count":75,"referenced_works":["https://openalex.org/W1180819604","https://openalex.org/W1481503809","https://openalex.org/W1567427264","https://openalex.org/W1738019091","https://openalex.org/W1754042689","https://openalex.org/W1854324009","https://openalex.org/W1854810044","https://openalex.org/W1963550288","https://openalex.org/W1966172022","https://openalex.org/W1969873373","https://openalex.org/W1969943857","https://openalex.org/W1971849220","https://openalex.org/W1973580557","https://openalex.org/W1974880836","https://openalex.org/W1975447903","https://openalex.org/W1980825524","https://openalex.org/W1981458288","https://openalex.org/W1986240377","https://openalex.org/W1988037271","https://openalex.org/W1994893070","https://openalex.org/W1995089645","https://openalex.org/W1996813166","https://openalex.org/W2008312146","https://openalex.org/W2017398555","https://openalex.org/W2024311391","https://openalex.org/W2025556769","https://openalex.org/W2026587946","https://openalex.org/W2029476353","https://openalex.org/W2033757486","https://openalex.org/W2036981634","https://openalex.org/W2038896140","https://openalex.org/W2041133307","https://openalex.org/W2060531713","https://openalex.org/W2061457917","https://openalex.org/W2061799302","https://openalex.org/W2063060349","https://openalex.org/W2067455153","https://openalex.org/W2078589566","https://openalex.org/W2079153029","https://openalex.org/W2079266488","https://openalex.org/W2095242270","https://openalex.org/W2095705004","https://openalex.org/W2096584150","https://openalex.org/W2102306034","https://openalex.org/W2103034037","https://openalex.org/W2103299776","https://openalex.org/W2112411768","https://openalex.org/W2121895929","https://openalex.org/W2123333780","https://openalex.org/W2132625528","https://openalex.org/W2146249493","https://openalex.org/W2152249789","https://openalex.org/W2154670681","https://openalex.org/W2155862582","https://openalex.org/W2157296083","https://openalex.org/W2171292751","https://openalex.org/W2213443318","https://openalex.org/W2223809533","https://openalex.org/W2234529989","https://openalex.org/W2267970559","https://openalex.org/W2271701161","https://openalex.org/W2271736303","https://openalex.org/W2278966645","https://openalex.org/W2285695389","https://openalex.org/W2289619256","https://openalex.org/W2298381644","https://openalex.org/W2301625241","https://openalex.org/W2306570595","https://openalex.org/W2321484219","https://openalex.org/W2332135472","https://openalex.org/W2407586185","https://openalex.org/W2411825743","https://openalex.org/W2515097834","https://openalex.org/W2999559191","https://openalex.org/W4245176872"],"related_works":["https://openalex.org/W4392059316","https://openalex.org/W4240532245","https://openalex.org/W3187200704","https://openalex.org/W3112966125","https://openalex.org/W2903287478","https://openalex.org/W2073233024","https://openalex.org/W2031259671","https://openalex.org/W1990832091","https://openalex.org/W1966443150","https://openalex.org/W1961356786"],"abstract_inverted_index":{"The":[0,32,67,149,171],"binding":[1],"affinities":[2,68],"(IC50)":[3],"reported":[4],"for":[5,93,190,197,209],"diverse":[6,107],"structural":[7,56,124],"and":[8,29,41,45,48,81,125,137,163,206],"chemical":[9,60,65,126],"classes":[10],"of":[11,58,104,122,131,173],"human":[12],"\u03b2-secretase":[13],"1":[14,169],"(BACE-1)":[15],"inhibitors":[16,192],"in":[17,23,62,89,156],"literature":[18,92],"were":[19,69],"modeled":[20,70],"using":[21,71],"multiple":[22],"silico":[24],"ligand":[25],"based":[26,177,187],"modeling":[27],"approaches":[28],"statistical":[30],"techniques.":[31],"descriptor":[33,176],"space":[34],"encompasses":[35],"simple":[36],"binary":[37],"molecular":[38,51],"fingerprint,":[39],"one-":[40],"two-dimensional":[42],"constitutional,":[43],"physicochemical,":[44],"topological":[46],"descriptors,":[47],"sophisticated":[49],"three-dimensional":[50],"fields":[52],"that":[53],"require":[54],"appropriate":[55],"alignments":[57],"varied":[59],"scaffolds":[61],"one":[63],"universal":[64],"space.":[66],"qualitative":[72,159],"classification":[73,160],"or":[74],"quantitative":[75,164],"regression":[76],"schemes":[77],"involving":[78],"linear,":[79],"nonlinear,":[80],"deep":[82],"neural":[83],"network":[84],"(DNN)":[85],"machine-learning":[86,150],"methods":[87,151,201],"used":[88,113,128],"the":[90,105,116,119,123,146,158,174,184,203],"scientific":[91],"quantitative-structure":[94],"activity":[95],"relationships":[96],"(QSAR).":[97],"In":[98],"a":[99,194],"departure":[100],"from":[101],"tradition,":[102],"\u223c20%":[103],"chemically":[106],"data":[108],"set":[109],"(205":[110],"compounds)":[111,136,141],"was":[112],"to":[114,144],"train":[115],"model":[117,147],"with":[118],"remaining":[120],"\u223c80%":[121],"analogs":[127],"as":[129,213],"part":[130],"an":[132],"external":[133],"validation":[134],"(1273":[135],"prospective":[138],"test":[139],"(69":[140],"sets":[142],"respectively":[143],"ascertain":[145],"performance.":[148],"investigated":[152],"herein":[153],"performed":[154],"well":[155],"both":[157],"(\u223c70%":[161],"accuracy)":[162],"IC50":[165],"predictions":[166],"(RMSE":[167],"\u223c":[168],"log).":[170],"success":[172],"2D":[175],"machine":[178],"learning":[179],"approach":[180],"when":[181],"compared":[182],"against":[183],"3D":[185],"field":[186],"technique":[188],"pursued":[189],"hBACE-1":[191],"provides":[193],"strong":[195],"impetus":[196],"systematically":[198],"applying":[199],"such":[200],"during":[202],"lead":[204],"identification":[205],"optimization":[207],"efforts":[208],"other":[210],"protein":[211],"families":[212],"well.":[214]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2461470610","counts_by_year":[{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":38},{"year":2022,"cited_by_count":38},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":9}],"updated_date":"2024-10-28T19:48:27.906291","created_date":"2016-07-22"}
