{"id":"https://openalex.org/W2042073740","doi":"https://doi.org/10.1002/jcc.540151106","title":"Reversed stereochemical preference in binding of Ro 31\u20108959 to HIV\u20101 proteinase: A free energy perturbation analysis","display_name":"Reversed stereochemical preference in binding of Ro 31\u20108959 to HIV\u20101 proteinase: A free energy perturbation analysis","publication_year":1994,"publication_date":"1994-11-01","ids":{"openalex":"https://openalex.org/W2042073740","doi":"https://doi.org/10.1002/jcc.540151106","mag":"2042073740"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.540151106","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540151106","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/A5013793637","display_name":"B. Govinda Rao","orcid":null},"institutions":[{"id":"https://openalex.org/I61970326","display_name":"Vertex Pharmaceuticals (United States)","ror":"https://ror.org/00anb1726","country_code":"US","type":"company","lineage":["https://openalex.org/I61970326"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"B. G. Rao","raw_affiliation_strings":["Vertex Pharmaceuticals Incorporated, 40 Allston Street, Cambridge, Massachusetts 02139"],"affiliations":[{"raw_affiliation_string":"Vertex Pharmaceuticals Incorporated, 40 Allston Street, Cambridge, Massachusetts 02139","institution_ids":["https://openalex.org/I61970326"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034115392","display_name":"Mark A. Murcko","orcid":"https://orcid.org/0000-0002-1235-2869"},"institutions":[{"id":"https://openalex.org/I61970326","display_name":"Vertex Pharmaceuticals (United States)","ror":"https://ror.org/00anb1726","country_code":"US","type":"company","lineage":["https://openalex.org/I61970326"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. A. Murcko","raw_affiliation_strings":["Vertex Pharmaceuticals Incorporated, 40 Allston Street, Cambridge, Massachusetts 02139"],"affiliations":[{"raw_affiliation_string":"Vertex Pharmaceuticals Incorporated, 40 Allston Street, Cambridge, Massachusetts 02139","institution_ids":["https://openalex.org/I61970326"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013793637"],"corresponding_institution_ids":["https://openalex.org/I61970326"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.4321,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.57894816,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"15","issue":"11","first_page":"1241","last_page":"1253"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9969000220298767,"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/preference","display_name":"Preference","score":0.5941295623779297},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"Free energy perturbation","score":0.5067227482795715},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.48523426055908203},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.42674893140792847},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.42245811223983765},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2561746835708618},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22660773992538452},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.13790041208267212},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.12702035903930664},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.11184614896774292}],"concepts":[{"id":"https://openalex.org/C2781249084","wikidata":"https://www.wikidata.org/wiki/Q908656","display_name":"Preference","level":2,"score":0.5941295623779297},{"id":"https://openalex.org/C162641036","wikidata":"https://www.wikidata.org/wiki/Q5500215","display_name":"Free energy perturbation","level":3,"score":0.5067227482795715},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48523426055908203},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.42674893140792847},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.42245811223983765},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2561746835708618},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22660773992538452},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.13790041208267212},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.12702035903930664},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11184614896774292}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/jcc.540151106","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540151106","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":[{"display_name":"Affordable and clean energy","score":0.6499999761581421,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W59009676","https://openalex.org/W620132579","https://openalex.org/W1487403006","https://openalex.org/W1603083519","https://openalex.org/W1637218542","https://openalex.org/W1965349185","https://openalex.org/W1966952510","https://openalex.org/W1968184943","https://openalex.org/W1976499671","https://openalex.org/W1978483079","https://openalex.org/W1979046104","https://openalex.org/W1981491253","https://openalex.org/W1982582136","https://openalex.org/W1995711216","https://openalex.org/W2005586076","https://openalex.org/W2016190213","https://openalex.org/W2019261111","https://openalex.org/W2026802618","https://openalex.org/W2030402747","https://openalex.org/W2031274716","https://openalex.org/W2031343308","https://openalex.org/W2038350697","https://openalex.org/W2041560550","https://openalex.org/W2066787645","https://openalex.org/W2077390552","https://openalex.org/W2079769193","https://openalex.org/W2082912027","https://openalex.org/W2086003834","https://openalex.org/W2087876594","https://openalex.org/W2089807142","https://openalex.org/W2093611233","https://openalex.org/W2102537419","https://openalex.org/W2102697248","https://openalex.org/W2106140689","https://openalex.org/W2107029002","https://openalex.org/W2114742412","https://openalex.org/W2128122374","https://openalex.org/W2133555349","https://openalex.org/W2148526417","https://openalex.org/W2160276605","https://openalex.org/W2215812048","https://openalex.org/W2949745155","https://openalex.org/W3004969213","https://openalex.org/W4235305170","https://openalex.org/W4244806755","https://openalex.org/W4252573137"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W2062208111","https://openalex.org/W19156051","https://openalex.org/W2019064984"],"abstract_inverted_index":{"Abstract":[0],"Ro":[1,105],"31\u20108959":[2,106],"is":[3,21,110,117],"a":[4,130,146,184],"highly":[5],"potent":[6],"inhibitor":[7,26],"of":[8,18,54,57,104,172,187],"HIV\u20101":[9],"proteinase":[10],"in":[11,83,102,118,155,183],"phase":[12],"III":[13],"clinical":[14],"trials":[15],"for":[16,49],"treatment":[17],"AIDS.":[19],"It":[20],"also":[22],"the":[23,33,47,50,58,62,65,75,80,84,95,98,122,126,135,141,152,162,169,204],"first":[24,63,96,142],"subnanomolar":[25],"that":[27,161],"demonstrated":[28],"reversed":[29],"stereochemical":[30,181],"preference":[31,48,182],"at":[32,88,151],"central":[34,66],"hydroxyl":[35,67,81],"group.":[36],"Free":[37],"energy":[38,100,148],"perturbation":[39],"calculations":[40],"have":[41,177],"been":[42],"carried":[43],"out":[44],"to":[45,112,140,176,190],"rationalize":[46],"R\u2010diastereomer":[51],"by":[52,193,216],"consideration":[53],"two":[55,163,170],"models":[56,171],"(weaker)":[59],"S\u2010diastereomer.":[60],"In":[61],"model,":[64,97,143],"group":[68,82,154],"makes":[69,87],"only":[70],"one":[71],"hydrogen":[72,92],"bond":[73],"with":[74,121,134],"active":[76,136],"site":[77,137],"aspartates,":[78],"whereas":[79],"second":[85,127],"model":[86,128],"least":[89],"three":[90],"strong":[91],"bonds.":[93],"Using":[94],"free":[99],"difference":[101],"binding":[103,201],"and":[107,168,196],"its":[108],"S\u2010diastereomer":[109,173],"calculated":[111],"be":[113,191],"3.4":[114],"kcal/mol,":[115],"which":[116],"close":[119],"agreement":[120],"experimental":[123],"value.":[124],"Although":[125],"has":[129,145],"more":[131],"favorable":[132],"interaction":[133],"aspartates":[138],"compared":[139],"it":[144],"higher":[147],"N\u2010axial":[149],"conformation":[150],"decahydroisoquinoline":[153],"P":[156],".":[157],"We":[158],"show":[159],"here":[160],"contributions":[164],"cancel":[165],"each":[166],"other":[167],"are":[174,208],"predicted":[175],"equivalent":[178],"binding.":[179],"The":[180,200],"hydroxyethylamine":[185],"series":[186],"inhibitors":[188,207],"appears":[189],"affected":[192],"both":[194],"intermolecular":[195],"intramolecular":[197],"(conformational)":[198],"energies.":[199],"data":[202],"on":[203,211],"proline":[205],"containing":[206],"rationalized":[209],"based":[210],"these":[212],"results.":[213],"\u00a9":[214],"1994":[215],"John":[217],"Wiley":[218],"&amp;":[219],"Sons,":[220],"Inc.":[221]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
