{"id":"https://openalex.org/W2163277225","doi":"https://doi.org/10.1021/ci300039a","title":"Four-Dimensional Structure\u2013Activity Relationship Model to Predict HIV-1 Integrase Strand Transfer Inhibition using LQTA-QSAR Methodology","display_name":"Four-Dimensional Structure\u2013Activity Relationship Model to Predict HIV-1 Integrase Strand Transfer Inhibition using LQTA-QSAR Methodology","publication_year":2012,"publication_date":"2012-06-04","ids":{"openalex":"https://openalex.org/W2163277225","doi":"https://doi.org/10.1021/ci300039a","mag":"2163277225","pmid":"https://pubmed.ncbi.nlm.nih.gov/22657398"},"language":"en","primary_location":{"id":"doi:10.1021/ci300039a","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300039a","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"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/A5058964473","display_name":"Eduardo Borges de Melo","orcid":"https://orcid.org/0000-0002-7455-1820"},"institutions":[{"id":"https://openalex.org/I193876067","display_name":"Universidade Estadual do Oeste do Paran\u00e1","ror":"https://ror.org/05ne20t07","country_code":"BR","type":"education","lineage":["https://openalex.org/I193876067"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Eduardo B. de Melo","raw_affiliation_strings":["Theoretical\rMedicinal and Environmental Chemistry Laboratory (LQMAT), Department\rof Pharmacy, Western Parana State University\u2212Unioeste, 2069 Universitaria St, Cascavel, PR, 85819-110, Brazil"],"affiliations":[{"raw_affiliation_string":"Theoretical\rMedicinal and Environmental Chemistry Laboratory (LQMAT), Department\rof Pharmacy, Western Parana State University\u2212Unioeste, 2069 Universitaria St, Cascavel, PR, 85819-110, Brazil","institution_ids":["https://openalex.org/I193876067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001869460","display_name":"M\u00e1rcia M. C. Ferreira","orcid":"https://orcid.org/0000-0001-5677-0299"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"M\u00e1rcia M. C. Ferreira","raw_affiliation_strings":["Laboratory for Theoretical and Applied\rChemometrics (LQTA), Institute of Chemistry, University of Campinas\u2212UNICAMP, P.O. Box 6154, Campinas,\rSP, 13084-971, Brazil"],"affiliations":[{"raw_affiliation_string":"Laboratory for Theoretical and Applied\rChemometrics (LQTA), Institute of Chemistry, University of Campinas\u2212UNICAMP, P.O. Box 6154, Campinas,\rSP, 13084-971, Brazil","institution_ids":["https://openalex.org/I181391015"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058964473"],"corresponding_institution_ids":["https://openalex.org/I193876067"],"apc_list":null,"apc_paid":null,"fwci":2.6956,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.90834538,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"52","issue":"7","first_page":"1722","last_page":"1732"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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 Drug Discovery Methods","score":0.9997000098228455,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9991000294685364,"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/T11440","display_name":"Click Chemistry and Applications","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/quantitative-structure\u2013activity-relationship","display_name":"Quantitative structure\u2013activity relationship","score":0.9208780527114868},{"id":"https://openalex.org/keywords/integrase","display_name":"Integrase","score":0.7637739181518555},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.5198355317115784},{"id":"https://openalex.org/keywords/integrase-inhibitor","display_name":"Integrase inhibitor","score":0.4857328534126282},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4298568069934845},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4050467312335968},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4030284583568573},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22919082641601562},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.1703294813632965},{"id":"https://openalex.org/keywords/antiretroviral-therapy","display_name":"Antiretroviral therapy","score":0.16270610690116882},{"id":"https://openalex.org/keywords/viral-load","display_name":"Viral load","score":0.06546396017074585}],"concepts":[{"id":"https://openalex.org/C164126121","wikidata":"https://www.wikidata.org/wiki/Q766383","display_name":"Quantitative structure\u2013activity relationship","level":2,"score":0.9208780527114868},{"id":"https://openalex.org/C14430832","wikidata":"https://www.wikidata.org/wiki/Q412550","display_name":"Integrase","level":3,"score":0.7637739181518555},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.5198355317115784},{"id":"https://openalex.org/C2777302000","wikidata":"https://www.wikidata.org/wiki/Q412251","display_name":"Integrase inhibitor","level":5,"score":0.4857328534126282},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4298568069934845},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4050467312335968},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4030284583568573},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22919082641601562},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.1703294813632965},{"id":"https://openalex.org/C2993143319","wikidata":"https://www.wikidata.org/wiki/Q583050","display_name":"Antiretroviral therapy","level":4,"score":0.16270610690116882},{"id":"https://openalex.org/C142462285","wikidata":"https://www.wikidata.org/wiki/Q2528140","display_name":"Viral load","level":3,"score":0.06546396017074585}],"mesh":[{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D004789","descriptor_name":"Enzyme Activation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019427","descriptor_name":"HIV Integrase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019427","descriptor_name":"HIV Integrase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019427","descriptor_name":"HIV Integrase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci300039a","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300039a","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:22657398","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22657398","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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8399999737739563,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W143962061","https://openalex.org/W1520276096","https://openalex.org/W1526205344","https://openalex.org/W1567204155","https://openalex.org/W1600632000","https://openalex.org/W1969743763","https://openalex.org/W1970034671","https://openalex.org/W1972016986","https://openalex.org/W1973660470","https://openalex.org/W1974622948","https://openalex.org/W1982110354","https://openalex.org/W1983128017","https://openalex.org/W1984073183","https://openalex.org/W1984811139","https://openalex.org/W1986688691","https://openalex.org/W1988978817","https://openalex.org/W1991057723","https://openalex.org/W1993180192","https://openalex.org/W1996656176","https://openalex.org/W2000993620","https://openalex.org/W2001413944","https://openalex.org/W2003835862","https://openalex.org/W2008517160","https://openalex.org/W2011703862","https://openalex.org/W2012026221","https://openalex.org/W2012752176","https://openalex.org/W2015145065","https://openalex.org/W2023792095","https://openalex.org/W2027363322","https://openalex.org/W2031828918","https://openalex.org/W2034570874","https://openalex.org/W2037926034","https://openalex.org/W2039528401","https://openalex.org/W2042909949","https://openalex.org/W2048156496","https://openalex.org/W2049879885","https://openalex.org/W2049894560","https://openalex.org/W2050310420","https://openalex.org/W2054716083","https://openalex.org/W2054758007","https://openalex.org/W2058251027","https://openalex.org/W2059863293","https://openalex.org/W2060921417","https://openalex.org/W2063060349","https://openalex.org/W2063889189","https://openalex.org/W2064645523","https://openalex.org/W2065048805","https://openalex.org/W2071901859","https://openalex.org/W2072692396","https://openalex.org/W2073031487","https://openalex.org/W2073503722","https://openalex.org/W2073953215","https://openalex.org/W2074681440","https://openalex.org/W2074956847","https://openalex.org/W2077454017","https://openalex.org/W2079198822","https://openalex.org/W2080154705","https://openalex.org/W2086190989","https://openalex.org/W2086383965","https://openalex.org/W2087466582","https://openalex.org/W2087661061","https://openalex.org/W2092880671","https://openalex.org/W2098524560","https://openalex.org/W2099988757","https://openalex.org/W2100349128","https://openalex.org/W2114367386","https://openalex.org/W2117813630","https://openalex.org/W2136382177","https://openalex.org/W2144906256","https://openalex.org/W2151582714","https://openalex.org/W2155032883","https://openalex.org/W2161422660","https://openalex.org/W2164186008","https://openalex.org/W2171711893","https://openalex.org/W2182777591","https://openalex.org/W2185870002","https://openalex.org/W2216783520","https://openalex.org/W2300957781","https://openalex.org/W2497229379","https://openalex.org/W2949951507","https://openalex.org/W4206211367","https://openalex.org/W4213151958","https://openalex.org/W4243645902","https://openalex.org/W4244209983"],"related_works":["https://openalex.org/W1489859663","https://openalex.org/W1994342377","https://openalex.org/W2125774028","https://openalex.org/W2106095665","https://openalex.org/W35520510","https://openalex.org/W2348191928","https://openalex.org/W2810278931","https://openalex.org/W2475003651","https://openalex.org/W2385936183","https://openalex.org/W1990411514"],"abstract_inverted_index":{"Despite":[0],"highly":[1],"active":[2],"antiretroviral":[3],"therapy":[4],"(HAART)":[5],"implementation,":[6],"there":[7],"is":[8,22,231],"a":[9,23,34,49,78,218,232],"continuous":[10],"need":[11],"to":[12,76,87,94,166,204,243],"search":[13],"for":[14,28,221],"new":[15,43,227],"anti-HIV":[16],"agents.":[17],"HIV-1":[18,54],"integrase":[19],"(HIV-1":[20],"IN)":[21],"recently":[24],"validated":[25],"biological":[26],"target":[27],"AIDS":[29],"therapy.":[30],"In":[31],"this":[32],"work,":[33],"four-dimensional":[35],"quantitative":[36],"structure-activity":[37],"relationship":[38],"(4D-QSAR)":[39],"study":[40],"using":[41,105],"the":[42,61,96,196,207,211,224],"methodology":[44],"named":[45],"LQTA-QSAR":[46,84,238],"approach":[47],"with":[48,206],"training":[50],"set":[51],"of":[52,195,226,235,237],"85":[53],"IN":[55],"strand":[56],"transfer":[57],"inhibitors":[58],"(INSTI),":[59],"containing":[60],"\u03b2-diketo":[62],"acid":[63],"(DKA)":[64],"substructure,":[65],"was":[66,74,85,164,177],"carried":[67],"out.":[68],"The":[69,99,161,214],"GROMACS":[70],"molecular":[71],"dynamic":[72],"package":[73],"used":[75,245],"obtain":[77],"conformational":[79],"ensemble":[80],"profile":[81],"(CEP)":[82],"and":[83,90,93,109,122,133,137,155,176,210,229],"employed":[86],"calculate":[88],"Coulomb":[89],"Lennard-Jones":[91],"potentials":[92],"generate":[95],"field":[97,107],"descriptors.":[98],"partial":[100],"least-squares":[101],"(PLS)":[102],"regression":[103],"model":[104,163,197,215],"14":[106],"descriptors":[108,202],"8":[110],"latent":[111],"variables":[112],"(LV)":[113],"yielded":[114],"satisfactory":[115],"statistics":[116],"(R2=":[117],"0.897,":[118],"SEC":[119],"=":[120,124,131,135,141,144,147,150,153,159,174,186,190],"0.270,":[121],"F":[123],"72.827),":[125],"good":[126,219],"performance":[127],"in":[128,223,246],"internal":[129],"(QLOO2":[130],"0.842":[132],"SEV":[134],"0.314)":[136],"external":[138],"prediction":[139],"(Rpred2":[140],"0.839,":[142],"SEP":[143],"0.384,":[145],"AREpred":[146],"4.942%,":[148],"k":[149],"0.981,":[151],"k\u2032":[152],"1.016,":[154],"|R02":[156],"\u2013":[157],"R0\u20322":[158],"0.0257).":[160],"QSAR":[162],"shown":[165],"be":[167,199,244],"robust":[168],"(leave-N-out":[169],"cross":[170],"validation;":[171],"average":[172],"QLNO2":[173],"0.834)":[175],"not":[178],"built":[179],"by":[180],"chance":[181],"(y-randomization":[182],"test;":[183],"R2":[184],"intercept":[185,189],"0.109;":[187],"Q2":[188],"-0.398).":[191],"Fair":[192],"chemical":[193],"interpretation":[194],"could":[198],"traced,":[200],"including":[201],"related":[203],"interaction":[205],"metallic":[208],"cofactors":[209],"hydrophobic":[212],"loop.":[213],"obtained":[216],"has":[217],"potential":[220],"aid":[222],"design":[225,249],"INSTI,":[228],"it":[230],"successful":[233],"example":[234],"application":[236],"as":[239],"an":[240],"useful":[241],"tool":[242],"computer-aided":[247],"drug":[248],"(CADD).":[250]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}