{"id":"https://openalex.org/W2019054779","doi":"https://doi.org/10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8","title":"Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease","display_name":"Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease","publication_year":2000,"publication_date":"2000-03-01","ids":{"openalex":"https://openalex.org/W2019054779","doi":"https://doi.org/10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8","mag":"2019054779"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8","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/A5101908866","display_name":"Laurent David","orcid":"https://orcid.org/0000-0003-3594-0353"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laurent David","raw_affiliation_strings":["Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","institution_ids":["https://openalex.org/I1321296531"]},{"raw_affiliation_string":"Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","institution_ids":["https://openalex.org/I1321296531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032088629","display_name":"Ray Luo","orcid":"https://orcid.org/0000-0002-6346-8271"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ray Luo","raw_affiliation_strings":["Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","institution_ids":["https://openalex.org/I1321296531"]},{"raw_affiliation_string":"Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","institution_ids":["https://openalex.org/I1321296531"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049982297","display_name":"Michael K. Gilson","orcid":"https://orcid.org/0000-0002-3375-1738"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael K. Gilson","raw_affiliation_strings":["Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","institution_ids":["https://openalex.org/I1321296531"]},{"raw_affiliation_string":"Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850","institution_ids":["https://openalex.org/I1321296531"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049982297"],"corresponding_institution_ids":["https://openalex.org/I1321296531"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":3.2266,"has_fulltext":false,"cited_by_count":103,"citation_normalized_percentile":{"value":0.92295585,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"4","first_page":"295","last_page":"309"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9993000030517578,"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":0.9972000122070312,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/hiv-1-protease","display_name":"HIV-1 protease","score":0.5700758695602417},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.5494510531425476},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5293912291526794},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.5190913677215576},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.49732187390327454},{"id":"https://openalex.org/keywords/nanosecond","display_name":"Nanosecond","score":0.4948248267173767},{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.4657880365848541},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.42696547508239746},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4145227074623108},{"id":"https://openalex.org/keywords/energetics","display_name":"Energetics","score":0.41023725271224976},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.371354341506958},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.36798328161239624},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.2092987298965454},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18045520782470703},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.15270742774009705},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07439246773719788},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance","display_name":"Nuclear magnetic resonance","score":0.0690787136554718}],"concepts":[{"id":"https://openalex.org/C2777583353","wikidata":"https://www.wikidata.org/wiki/Q410261","display_name":"HIV-1 protease","level":4,"score":0.5700758695602417},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.5494510531425476},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5293912291526794},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.5190913677215576},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.49732187390327454},{"id":"https://openalex.org/C51141536","wikidata":"https://www.wikidata.org/wiki/Q838801","display_name":"Nanosecond","level":3,"score":0.4948248267173767},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.4657880365848541},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.42696547508239746},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4145227074623108},{"id":"https://openalex.org/C97514900","wikidata":"https://www.wikidata.org/wiki/Q719597","display_name":"Energetics","level":2,"score":0.41023725271224976},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.371354341506958},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.36798328161239624},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.2092987298965454},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18045520782470703},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.15270742774009705},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07439246773719788},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0690787136554718},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C520434653","wikidata":"https://www.wikidata.org/wiki/Q38867","display_name":"Laser","level":2,"score":0.0},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(200003)21:4<295::aid-jcc5>3.0.co;2-8","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":[{"score":0.5699999928474426,"display_name":"No poverty","id":"https://metadata.un.org/sdg/1"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1963675638","https://openalex.org/W1970111528","https://openalex.org/W1971110562","https://openalex.org/W1975289752","https://openalex.org/W1978084071","https://openalex.org/W1980381306","https://openalex.org/W1984231149","https://openalex.org/W1988247756","https://openalex.org/W1988613096","https://openalex.org/W1995842153","https://openalex.org/W1997639796","https://openalex.org/W1998980954","https://openalex.org/W2003542620","https://openalex.org/W2004188337","https://openalex.org/W2010849549","https://openalex.org/W2013829952","https://openalex.org/W2016563610","https://openalex.org/W2020002894","https://openalex.org/W2020561870","https://openalex.org/W2024243556","https://openalex.org/W2025324398","https://openalex.org/W2027638447","https://openalex.org/W2027978582","https://openalex.org/W2028462745","https://openalex.org/W2031170108","https://openalex.org/W2037018193","https://openalex.org/W2037274248","https://openalex.org/W2039665613","https://openalex.org/W2047730466","https://openalex.org/W2048744137","https://openalex.org/W2053096100","https://openalex.org/W2058052041","https://openalex.org/W2060304556","https://openalex.org/W2061259478","https://openalex.org/W2064747164","https://openalex.org/W2075369230","https://openalex.org/W2076097518","https://openalex.org/W2098344108","https://openalex.org/W2107572441","https://openalex.org/W2116775268","https://openalex.org/W2116929165","https://openalex.org/W2117092343","https://openalex.org/W2127116852","https://openalex.org/W2134418875","https://openalex.org/W2134731229","https://openalex.org/W2136371489","https://openalex.org/W2161288709","https://openalex.org/W2162166182","https://openalex.org/W2177731497","https://openalex.org/W4237543877","https://openalex.org/W4247951394"],"related_works":["https://openalex.org/W2135769142","https://openalex.org/W2392683545","https://openalex.org/W2079485067","https://openalex.org/W2129187661","https://openalex.org/W3161520842","https://openalex.org/W1598419000","https://openalex.org/W1973740172","https://openalex.org/W2034505458","https://openalex.org/W2084685050","https://openalex.org/W1174063231"],"abstract_inverted_index":{"This":[0],"study":[1],"characterizes":[2],"the":[3,17,29,55,62,84,117,120,123,127,131,141,149,153],"accuracy":[4],"of":[5,28,76,105,119,126],"energies":[6,71],"and":[7,16,42,69,143],"forces":[8,81],"computed":[9,82],"with":[10,22,46,52,83,108],"a":[11,37],"generalized":[12],"Born":[13],"(GB)":[14],"model":[15,21,86,94],"distance-dependent":[18],"dielectric":[19],"(DDD)":[20],"respect":[23],"to":[24,115],"detailed":[25],"finite":[26],"solutions":[27],"Poisson":[30],"equation":[31],"(FDPE).":[32],"Tests":[33],"are":[34,87,113],"done":[35],"for":[36,43,54,61,122],"small":[38,56],"molecule":[39],"in":[40,74,140,152],"solution":[41],"HIV-1":[44,106],"protease":[45,107],"inhibitor,":[47],"KNI-272.":[48],"GB":[49,68,85,144],"agrees":[50],"well":[51,60],"FDPE":[53,70,142],"molecule,":[57],"but":[58,146],"less":[59,88,97],"protein":[63],"system.":[64],"The":[65,92],"correlation":[66],"between":[67],"is":[72,95],"poorest":[73],"calculations":[75],"changes":[77],"upon":[78],"binding.":[79],"Also,":[80],"accurate":[89,98],"than":[90,99],"energies.":[91],"DDD":[93,154],"far":[96],"GB.":[100],"Nanosecond":[101],"stochastic":[102],"dynamics":[103],"simulations":[104,145],"an":[109],"empty":[110],"active":[111,128,132,150],"site":[112,133,151],"used":[114],"examine":[116],"consequence":[118],"models":[121],"conformational":[124],"preferences":[125],"site.":[129],"Interestingly,":[130],"flaps":[134],"remain":[135],"near":[136],"their":[137],"starting":[138],"conformations":[139],"collapse":[147],"into":[148],"simulation.":[155],"\u00a9":[156],"2000":[157,168],"John":[158],"Wiley":[159],"&":[160],"Sons,":[161],"Inc.":[162],"J":[163],"Comput":[164],"Chem":[165],"21:":[166],"295\u2013309,":[167]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
