{"id":"https://openalex.org/W2031204530","doi":"https://doi.org/10.1002/jcc.540150108","title":"Simulations of the solution structure of HIV\u20101 protease in the presence and absence of bound zinc","display_name":"Simulations of the solution structure of HIV\u20101 protease in the presence and absence of bound zinc","publication_year":1994,"publication_date":"1994-01-01","ids":{"openalex":"https://openalex.org/W2031204530","doi":"https://doi.org/10.1002/jcc.540150108","mag":"2031204530"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.540150108","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540150108","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5076436548","display_name":"Darrin M. York","orcid":"https://orcid.org/0000-0002-9193-7055"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"D. M. York","raw_affiliation_strings":["Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599-3290","Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709","Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599\u20103290"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599-3290","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709","institution_ids":["https://openalex.org/I4210095140"]},{"raw_affiliation_string":"Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599\u20103290","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077725607","display_name":"Libero J. Bartolotti","orcid":"https://orcid.org/0000-0003-4155-5048"},"institutions":[{"id":"https://openalex.org/I2799790446","display_name":"North Carolina Biotechnology Center","ror":"https://ror.org/03hj4jr80","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799790446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L. J. Bartolotti","raw_affiliation_strings":["North Carolina Supercomputing Center, a Division of MCNC, Research Triangle Park, North Carolina 27709"],"affiliations":[{"raw_affiliation_string":"North Carolina Supercomputing Center, a Division of MCNC, Research Triangle Park, North Carolina 27709","institution_ids":["https://openalex.org/I2799790446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108489476","display_name":"Tom Darden","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. A. Darden","raw_affiliation_strings":["Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709","institution_ids":["https://openalex.org/I4210095140"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008226395","display_name":"Lee G. Pedersen","orcid":"https://orcid.org/0000-0003-1262-9861"},"institutions":[{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]},{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L. G. Pedersen","raw_affiliation_strings":["Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599-3290","Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709","Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599\u20103290"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599-3290","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709","institution_ids":["https://openalex.org/I4210095140"]},{"raw_affiliation_string":"Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599\u20103290","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108456497","display_name":"M W Anderson","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. W. Anderson","raw_affiliation_strings":["Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709"],"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709","institution_ids":["https://openalex.org/I4210095140"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5076436548"],"corresponding_institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4210095140"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.7309,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.69951702,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"15","issue":"1","first_page":"61","last_page":"71"},"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":0.9983999729156494,"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":0.9983999729156494,"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/T10112","display_name":"HIV Research and Treatment","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10570","display_name":"Drug Transport and Resistance Mechanisms","score":0.9873999953269958,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.802432656288147},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.7942789793014526},{"id":"https://openalex.org/keywords/zinc","display_name":"Zinc","score":0.7827804088592529},{"id":"https://openalex.org/keywords/dimer","display_name":"Dimer","score":0.6668752431869507},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5411436557769775},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.5090165138244629},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.4828363060951233},{"id":"https://openalex.org/keywords/hiv-1-protease","display_name":"HIV-1 protease","score":0.4574001431465149},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.42324453592300415},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.42164671421051025},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.3761374056339264},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3265776038169861},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.3134296238422394},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14715877175331116},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07043305039405823}],"concepts":[{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.802432656288147},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7942789793014526},{"id":"https://openalex.org/C535196362","wikidata":"https://www.wikidata.org/wiki/Q758","display_name":"Zinc","level":2,"score":0.7827804088592529},{"id":"https://openalex.org/C2779546866","wikidata":"https://www.wikidata.org/wiki/Q531306","display_name":"Dimer","level":2,"score":0.6668752431869507},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5411436557769775},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.5090165138244629},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4828363060951233},{"id":"https://openalex.org/C2777583353","wikidata":"https://www.wikidata.org/wiki/Q410261","display_name":"HIV-1 protease","level":4,"score":0.4574001431465149},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.42324453592300415},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.42164671421051025},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.3761374056339264},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3265776038169861},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.3134296238422394},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14715877175331116},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07043305039405823},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/jcc.540150108","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540150108","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W593906914","https://openalex.org/W1479894082","https://openalex.org/W1519899019","https://openalex.org/W1599308119","https://openalex.org/W1963675638","https://openalex.org/W1968484323","https://openalex.org/W1976499671","https://openalex.org/W1978928219","https://openalex.org/W1979046104","https://openalex.org/W1979853118","https://openalex.org/W1986248827","https://openalex.org/W1989475707","https://openalex.org/W1992074936","https://openalex.org/W1995396220","https://openalex.org/W2004708900","https://openalex.org/W2007608151","https://openalex.org/W2008708467","https://openalex.org/W2011805684","https://openalex.org/W2028124297","https://openalex.org/W2030402747","https://openalex.org/W2033553403","https://openalex.org/W2053410564","https://openalex.org/W2063045805","https://openalex.org/W2069146496","https://openalex.org/W2070368233","https://openalex.org/W2077195277","https://openalex.org/W2082912027","https://openalex.org/W2090446375","https://openalex.org/W2123166384","https://openalex.org/W2124660391","https://openalex.org/W2137364876","https://openalex.org/W2146946460","https://openalex.org/W2155524113","https://openalex.org/W2165732545","https://openalex.org/W2474658456","https://openalex.org/W2949745155"],"related_works":["https://openalex.org/W2049250591","https://openalex.org/W2126525653","https://openalex.org/W1516237426","https://openalex.org/W2256372280","https://openalex.org/W4245621070","https://openalex.org/W1969009510","https://openalex.org/W1973441633","https://openalex.org/W2801493643","https://openalex.org/W2075748968","https://openalex.org/W2128025541"],"abstract_inverted_index":{"Abstract":[0],"Zinc":[1],"ions":[2],"have":[3,102],"been":[4,103],"shown":[5],"to":[6,106,116,159],"inhibit":[7],"human":[8],"immunodeficiency":[9],"virus":[10],"type":[11],"1":[12],"(HIV\u20101)":[13],"protease":[14,81],"in":[15,41,85,92,198],"vitro":[16],"at":[17,99,167,187],"neutral":[18],"pH":[19],"[Zhang":[20],"et":[21,61,143],"al.":[22,62,144],"Biochemistry":[23],",":[24,26,64,66],"36":[25],"8717":[27],"(1991)].":[28],"Kinetic":[29],"data":[30,135],"from":[31],"this":[32,72,100,152],"study":[33],"support":[34],"a":[35],"reversible":[36],"binding":[37,155,166],"mechanism":[38],"of":[39,47,56,79,97,123,129,164],"zinc":[40,83,98,112,165],"the":[42,48,54,57,77,86,93,117,124,130,154,168,199],"active":[43,87,131,169],"site.":[44],"Preliminary":[45],"calculations":[46,175],"ion\u2013protein":[49],"potential":[50],"energy":[51],"based":[52,171],"on":[53,172],"geometry":[55],"crystallographic":[58],"structure":[59,78],"[Wlodawer":[60],"Science":[63],"245":[65],"616":[67],"(1989)]":[68],"are":[69,136],"consistent":[70,137],"with":[71,82,138,182],"proposed":[73,162],"mechanism.":[74],"To":[75],"examine":[76],"HIV\u20101":[80],"bound":[84,115],"site,":[88],"molecular":[89],"dynamics":[90],"simulations":[91,110],"presence":[94],"and":[95,146],"absence":[96],"site":[101,132,156,170],"carried":[104],"out":[105],"200":[107],"ps.":[108],"These":[109,134],"suggest":[111],"remains":[113],"stably":[114],"catalytic":[118,184],"aspartate":[119],"residues":[120],"without":[121],"disruption":[122],"dimer":[125],"or":[126],"significant":[127],"alteration":[128],"structure.":[133],"those":[139],"observed":[140],"by":[141,195,203],"Zhang":[142],"(1991),":[145],"together":[147],"give":[148],"strong":[149],"evidence":[150],"that":[151,157],"is":[153,180],"leads":[158],"inactivation.":[160],"A":[161],"model":[163],"quantum":[173],"mechanical":[174],"indicates":[176],"Zn":[177],"+2":[178],"coordination":[179],"monodentate":[181],"each":[183],"aspartate,":[185],"leaving":[186],"least":[188],"two":[189],"ligand":[190],"positions":[191],"potentially":[192],"free":[193],"(occupied":[194],"water":[196],"molecules":[197],"calculations).":[200],"\u00a9":[201],"1994":[202],"John":[204],"Wiley":[205],"&amp;":[206],"Sons,":[207],"Inc.":[208]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
