{"id":"https://openalex.org/W2514402431","doi":"https://doi.org/10.1021/acs.jcim.6b00393","title":"Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de Novo Docking of First- and Second-Generation Small-Molecule CD4 Mimics","display_name":"Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de Novo Docking of First- and Second-Generation Small-Molecule CD4 Mimics","publication_year":2016,"publication_date":"2016-09-07","ids":{"openalex":"https://openalex.org/W2514402431","doi":"https://doi.org/10.1021/acs.jcim.6b00393","mag":"2514402431","pmid":"https://pubmed.ncbi.nlm.nih.gov/27602436"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00393","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00393","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/A5059258417","display_name":"Francesca Moraca","orcid":"https://orcid.org/0000-0003-0248-9834"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Francesca Moraca","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103020726","display_name":"Kriti Acharya","orcid":"https://orcid.org/0000-0002-3408-149X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kriti Acharya","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076700953","display_name":"Bruno Melillo","orcid":"https://orcid.org/0000-0002-9708-5287"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruno Melillo","raw_affiliation_strings":["Department\rof Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States"],"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066527875","display_name":"Amos B. Smith","orcid":"https://orcid.org/0000-0002-1712-8567"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amos B. Smith","raw_affiliation_strings":["Department\rof Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States"],"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013936515","display_name":"Irwin Chaiken","orcid":"https://orcid.org/0000-0002-2996-2030"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Irwin Chaiken","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5038508476","display_name":"Cameron F. Abrams","orcid":"https://orcid.org/0000-0002-1240-0816"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cameron F. Abrams","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5059258417"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2341,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.79898336,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"56","issue":"10","first_page":"2069","last_page":"2079"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":1.0,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9987999796867371,"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/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9898999929428101,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7401897311210632},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.6491484642028809},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5943925976753235},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.5137292146682739},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.44746407866477966},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.35140931606292725},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.35116398334503174},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3473395109176636},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2553304433822632},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22160261869430542},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.14733532071113586},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07135877013206482}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7401897311210632},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.6491484642028809},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5943925976753235},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.5137292146682739},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.44746407866477966},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.35140931606292725},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.35116398334503174},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3473395109176636},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2553304433822632},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22160261869430542},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.14733532071113586},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07135877013206482},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","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}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054299","descriptor_name":"env Gene Products, Human Immunodeficiency Virus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054299","descriptor_name":"env Gene Products, Human Immunodeficiency Virus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054299","descriptor_name":"env Gene Products, Human Immunodeficiency Virus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054299","descriptor_name":"env Gene Products, Human Immunodeficiency Virus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054299","descriptor_name":"env Gene Products, Human Immunodeficiency Virus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054299","descriptor_name":"env Gene Products, Human Immunodeficiency Virus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.6b00393","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00393","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:27602436","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27602436","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},{"id":"pmh:oai:europepmc.org:4567630","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5206489","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,"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"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5199999809265137,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G6502549079","display_name":null,"funder_award_id":"GM-056550","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"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":32,"referenced_works":["https://openalex.org/W1543687584","https://openalex.org/W1944617745","https://openalex.org/W1977482735","https://openalex.org/W1983745950","https://openalex.org/W1985034086","https://openalex.org/W1985588649","https://openalex.org/W1990724722","https://openalex.org/W1992984464","https://openalex.org/W1994383375","https://openalex.org/W2000885937","https://openalex.org/W2003422665","https://openalex.org/W2009423060","https://openalex.org/W2027408247","https://openalex.org/W2027423337","https://openalex.org/W2027578254","https://openalex.org/W2029667189","https://openalex.org/W2039613640","https://openalex.org/W2043701535","https://openalex.org/W2044790939","https://openalex.org/W2048556083","https://openalex.org/W2051775752","https://openalex.org/W2072802103","https://openalex.org/W2074179519","https://openalex.org/W2077496215","https://openalex.org/W2086974099","https://openalex.org/W2098781795","https://openalex.org/W2102377211","https://openalex.org/W2141666704","https://openalex.org/W2143135287","https://openalex.org/W2150981663","https://openalex.org/W2318401834","https://openalex.org/W2342089851"],"related_works":["https://openalex.org/W4312103688","https://openalex.org/W2575434942","https://openalex.org/W2047838177","https://openalex.org/W2329052364","https://openalex.org/W2064383522","https://openalex.org/W3113347309","https://openalex.org/W4282913408","https://openalex.org/W2584261332","https://openalex.org/W4243322502","https://openalex.org/W2037320233"],"abstract_inverted_index":{"Small-molecule":[0],"CD4":[1,163],"mimics":[2],"(SMCM's)":[3],"bind":[4],"to":[5,19,91,104,137,210,229],"the":[6,10,28,34,37,45,49,105,126,131,139,151,177,180,196,204,218,224],"gp120":[7,51,153,172,200],"subunit":[8],"of":[9,27,36,48,64,74,79,97,101,130,142,226,237],"HIV-1":[11],"envelope":[12],"glycoprotein":[13],"(Env)":[14],"and":[15,30,33,39,86,94,99,112,116,167,199],"have":[16],"been":[17,208],"optimized":[18,209],"block":[20],"cell":[21],"infection":[22],"in":[23,44,127,144,162],"vitro.":[24],"The":[25,155],"lack":[26],"V1/2":[29,115],"V3":[31,117],"loops":[32,118],"presence":[35],"\u03b22/3":[38],"\u03b220/21":[40],"strands":[41],"(bridging":[42],"sheet)":[43],"available":[46],"structures":[47,110],"monomeric":[50,152],"core":[52,173,201],"may":[53],"limit":[54],"its":[55],"applicability":[56],"as":[57],"a":[58,72,185,234],"target":[59,187],"for":[60,188],"further":[61,189],"synthetic":[62],"optimization":[63,191],"SMCM":[65,143],"potency":[66],"and/or":[67],"breadth.":[68],"Here,":[69],"we":[70],"employ":[71],"combination":[73],"binding-site":[75],"search,":[76],"docking,":[77],"estimation":[78],"protein-ligand":[80],"interaction":[81],"energy,":[82],"all-atom":[83],"molecular":[84],"dynamics,":[85],"ELISA-based":[87],"CD4-binding":[88],"competition":[89,165],"assays":[90],"create,":[92],"characterize,":[93],"rationalize":[95],"models":[96],"first-":[98],"second-generation":[100],"SMCM's":[102,190,232],"bound":[103],"distinct,":[106],"trimeric":[107,182],"BG505":[108],"SOSIP.664":[109],"4NCO":[111,181],"4TVP":[113,197],"containing":[114],"with":[119,159,168,192,217,233],"no":[120],"bridging":[121],"sheet.":[122],"We":[123],"demonstrate":[124],"that":[125,179,213],"silico":[128],"neutralization":[129],"highly":[132,219],"conserved":[133,220],"D368":[134],"is":[135],"necessary":[136],"obtain":[138],"correct":[140],"orientation":[141],"their":[145],"binding":[146,164],"site":[147],"when":[148],"docking":[149,205],"against":[150],"core.":[154],"computational":[156],"results":[157],"correlate":[158],"IC<sub>50</sub>'s":[160],"measured":[161,170],"ELISA":[166],"K<sub>D</sub>'s":[169],"on":[171],"monomer.":[174,202],"This":[175],"supports":[176],"hypothesis":[178],"structure":[183],"represents":[184],"viable":[186],"advantages":[193],"over":[194],"both":[195],"trimer":[198],"Finally,":[203],"protocol":[206],"has":[207],"screen":[211],"compounds":[212],"can":[214],"clearly":[215],"interact":[216],"residue":[221],"D368,":[222],"increasing":[223],"likelihood":[225],"future":[227],"optimizations":[228],"arrive":[230],"at":[231],"broader":[235],"spectrum":[236],"activity.":[238]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}