{"id":"https://openalex.org/W2010563282","doi":"https://doi.org/10.1021/ct300957x","title":"Conformational Analysis and Parallel QM/MM X-ray Refinement of Protein Bound Anti-Alzheimer Drug Donepezil","display_name":"Conformational Analysis and Parallel QM/MM X-ray Refinement of Protein Bound Anti-Alzheimer Drug Donepezil","publication_year":2013,"publication_date":"2013-02-18","ids":{"openalex":"https://openalex.org/W2010563282","doi":"https://doi.org/10.1021/ct300957x","mag":"2010563282","pmid":"https://pubmed.ncbi.nlm.nih.gov/23526889"},"language":"en","primary_location":{"id":"doi:10.1021/ct300957x","doi":"https://doi.org/10.1021/ct300957x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ct300957x","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"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 Theory and Computation","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3601759","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101552747","display_name":"Zheng Fu","orcid":"https://orcid.org/0000-0002-7483-832X","observed_orcids":["https://orcid.org/0000-0002-7483-832X"]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zheng Fu","raw_affiliation_strings":["Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100372181","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-0642-6622","observed_orcids":["https://orcid.org/0000-0002-0642-6622"]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xue Li","raw_affiliation_strings":["Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida, 32611-8435, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida, 32611-8435, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002807978","display_name":"Yipu Miao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yipu Miao","raw_affiliation_strings":["Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida, 32611-8435, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida, 32611-8435, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085994852","display_name":"Kenneth M. Merz","orcid":"https://orcid.org/0000-0001-9139-5893","observed_orcids":["https://orcid.org/0000-0001-9139-5893"]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kenneth M. Merz","raw_affiliation_strings":["Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida, 32611-8435, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project,\r2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435,\rUnited States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida, 32611-8435, United States","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5085994852"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":1.1947,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.77082057,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"9","issue":"3","first_page":"1686","last_page":"1693"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.5493000149726868,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.5493000149726868,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12023","display_name":"Cholinesterase and Neurodegenerative Diseases","score":0.2506999969482422,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"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":0.09229999780654907,"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/donepezil","display_name":"donepezil","score":1.0},{"id":"https://openalex.org/keywords/acetylcholinesterase","display_name":"acetylcholinesterase","score":0.996999979019165},{"id":"https://openalex.org/keywords/alzheimer-s-disease","display_name":"Alzheimer's disease","score":0.6779999732971191},{"id":"https://openalex.org/keywords/conformational-analysis","display_name":"conformational analysis","score":0.8109999895095825},{"id":"https://openalex.org/keywords/conformational-energy-surface","display_name":"conformational energy surface","score":0.7789999842643738},{"id":"https://openalex.org/keywords/active-site-gorge","display_name":"active site gorge","score":0.5019999742507935},{"id":"https://openalex.org/keywords/m06-functional","display_name":"M06 functional","score":0.6240000128746033}],"concepts":[{"id":"https://openalex.org/C2780904820","wikidata":"https://www.wikidata.org/wiki/Q415081","display_name":"Donepezil","level":4,"score":0.9760526418685913},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8517789840698242},{"id":"https://openalex.org/C2778816929","wikidata":"https://www.wikidata.org/wiki/Q22676679","display_name":"Acetylcholinesterase","level":3,"score":0.7536970376968384},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4422374963760376},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4281710684299469},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42704808712005615},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3875950276851654},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2286873161792755},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14287734031677246},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13394179940223694},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.11100420355796814},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.08210587501525879},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C2779483572","wikidata":"https://www.wikidata.org/wiki/Q83030","display_name":"Dementia","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1021/ct300957x","doi":"https://doi.org/10.1021/ct300957x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ct300957x","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"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 Theory and Computation","raw_type":"journal-article"},{"id":"pmid:23526889","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23526889","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,"listed_in":[],"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 theory and computation","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:3221183","doi":null,"is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3601759","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3601759","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3601759","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Theory Comput","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:3601759","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3601759","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Theory Comput","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.428600013256073}],"sustainable_development_goals_aurora":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4699999988079071}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2265436241","display_name":"Metalloenzyme Structure and Function","funder_award_id":"R01GM044974","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5077032726","display_name":"Enhancement and Deployment of the Quantum Mechanical NMR Pose Scoring Method","funder_award_id":"R42GM075636","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5120358230","display_name":"Enhancement and Deployment of the Quantum Mechanical X-ray Refinement Model","funder_award_id":"R44GM079899","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8642784320","display_name":null,"funder_award_id":"R01 GM066859","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320310009","display_name":"University of Florida","ror":"https://ror.org/02y3ad647"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W72177144","https://openalex.org/W1972558086","https://openalex.org/W1979260280","https://openalex.org/W1987333298","https://openalex.org/W1990642173","https://openalex.org/W1993672505","https://openalex.org/W1994067502","https://openalex.org/W1995017064","https://openalex.org/W2000416127","https://openalex.org/W2002755329","https://openalex.org/W2007050333","https://openalex.org/W2012616191","https://openalex.org/W2013177991","https://openalex.org/W2013350002","https://openalex.org/W2015160568","https://openalex.org/W2020983121","https://openalex.org/W2028557359","https://openalex.org/W2032316350","https://openalex.org/W2040244904","https://openalex.org/W2041361334","https://openalex.org/W2041819327","https://openalex.org/W2046427207","https://openalex.org/W2047095305","https://openalex.org/W2055727638","https://openalex.org/W2056061015","https://openalex.org/W2061525157","https://openalex.org/W2065741910","https://openalex.org/W2070883565","https://openalex.org/W2076664119","https://openalex.org/W2080102154","https://openalex.org/W2085958374","https://openalex.org/W2091572890","https://openalex.org/W2096196180","https://openalex.org/W2098277049","https://openalex.org/W2099833638","https://openalex.org/W2107849704","https://openalex.org/W2112522119","https://openalex.org/W2116426967","https://openalex.org/W2119489910","https://openalex.org/W2126247854","https://openalex.org/W2126813062","https://openalex.org/W2137777161","https://openalex.org/W2149305458","https://openalex.org/W4248343095","https://openalex.org/W4253975223"],"related_works":["https://openalex.org/W1967518376","https://openalex.org/W2081638043","https://openalex.org/W4388901578","https://openalex.org/W1994111383","https://openalex.org/W1991778621","https://openalex.org/W2044324006","https://openalex.org/W1970435430","https://openalex.org/W1964384985","https://openalex.org/W1990209859","https://openalex.org/W1985888471"],"abstract_inverted_index":{"The":[0,87,192],"recognition":[1],"and":[2,39,68,83,158,202,213],"association":[3],"of":[4,19,37,65,150,153,173,194,210,216],"donepezil":[5,38,132,157,183],"with":[6,69],"acetylcholinesterase":[7],"(AChE)":[8],"has":[9],"been":[10],"extensively":[11],"studied":[12],"in":[13,117,139,164,181],"the":[14,20,34,42,62,70,77,112,124,129,140,151,154,159,165,174,182,188,195,207],"past":[15],"several":[16],"decades":[17],"because":[18],"former\u2019s":[21],"use":[22],"as":[23],"a":[24,96,118,171,178],"palliative":[25,214],"treatment":[26],"for":[27,206],"mild":[28],"Alzheimer":[29,217],"disease.":[30,218],"Herein,":[31],"we":[32,40],"examine":[33],"conformational":[35,56,184],"properties":[36],"re-examine":[41],"donepezil-AChE":[43,88],"crystal":[44],"structure":[45],"using":[46,61,76],"combined":[47],"quantum":[48],"mechanical/molecular":[49],"mechanical":[50],"(QM/MM)":[51],"X-ray":[52,99],"refinement":[53,100],"tools.":[54],"Donepezil\u2019s":[55],"energy":[57,186],"surface":[58],"was":[59,92,177],"explored":[60],"M06":[63],"suite":[64],"density":[66],"functionals":[67],"MP2/complete":[71],"basis":[72,85],"set":[73],"(CBS)":[74],"method":[75],"aug-cc-pVXZ":[78],"(":[79],"X":[80],"=":[81],"D":[82],"T)":[84],"sets.":[86],"complex":[89],"(PDB":[90],"1EVE)":[91],"also":[93],"rerefined":[94,131],"through":[95],"parallel":[97],"QM/MM":[98,130],"approach":[101],"based":[102],"on":[103],"an":[104,148],"in-house":[105],"ab":[106],"initio":[107],"code":[108],"QUICK,":[109],"which":[110],"uses":[111],"message":[113],"passing":[114],"interface":[115],"(MPI)":[116],"distributed":[119],"SCF":[120],"algorithm":[121],"to":[122,147],"accelerate":[123],"calculation":[125],"via":[126],"parallelization.":[127],"In":[128],"structure,":[133],"coordinate":[134],"errors":[135],"that":[136],"previously":[137],"existed":[138],"PDB":[141,190],"deposited":[142],"geometry":[143],"were":[144],"improved":[145],"leading":[146],"improvement":[149],"modeling":[152],"interaction":[155],"between":[156],"aromatic":[160],"side":[161],"chains":[162],"located":[163],"AChE":[166],"active":[167],"site":[168],"gorge.":[169],"As":[170],"result":[172],"rerefinement":[175],"there":[176],"93%":[179],"reduction":[180],"strain":[185],"versus":[187],"original":[189],"structure.":[191],"results":[193],"present":[196],"effort":[197],"offer":[198],"further":[199],"detailed":[200],"structural":[201],"biochemical":[203],"inhibitor-AChE":[204],"information":[205],"continued":[208],"development":[209],"more":[211],"effective":[212],"treatments":[215]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2025-10-10T00:00:00"}
