{"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":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]},{"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":"Francesca Moraca","raw_affiliation_strings":["Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103020726","display_name":"Kriti Acharya","orcid":"https://orcid.org/0000-0002-3408-149X"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]},{"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":"Kriti Acharya","raw_affiliation_strings":["Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I72816309"]}]},{"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]},{"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":"Irwin Chaiken","raw_affiliation_strings":["Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038508476","display_name":"Cameron F. Abrams","orcid":"https://orcid.org/0000-0002-1240-0816"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]},{"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":true,"raw_author_name":"Cameron F. Abrams","raw_affiliation_strings":["Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"\u2020 Department of Chemical and Biological Engineering and \u00a7 Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania 19104, United States","institution_ids":["https://openalex.org/I72816309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038508476"],"corresponding_institution_ids":["https://openalex.org/I72816309","https://openalex.org/I79576946"],"apc_list":null,"apc_paid":null,"fwci":1.1875,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.79150702,"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":[{"score":0.5199999809265137,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G4903788600","display_name":null,"funder_award_id":"GM 056550","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G979994218","display_name":null,"funder_award_id":"P01-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":[1,165],"mimics":[2],"(SMCM\u2019s)":[3],"bind":[4],"to":[5,19,91,104,137,214,233],"the":[6,10,28,34,37,45,49,105,126,131,139,151,181,184,200,208,222,228],"gp120":[7,51,153,176,204],"subunit":[8],"of":[9,27,36,48,64,74,79,97,101,130,142,230,241],"HIV-1":[11],"envelope":[12],"glycoprotein":[13],"(Env)":[14],"and":[15,30,33,39,86,94,99,112,116,169,203],"have":[16],"been":[17,212],"optimized":[18,213],"block":[20],"cell":[21],"infection":[22],"in":[23,44,127,144,164],"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":[52,177,205],"may":[53],"limit":[54],"its":[55],"applicability":[56],"as":[57],"a":[58,72,189,238],"target":[59,191],"for":[60,192],"further":[61,193],"synthetic":[62],"optimization":[63,195],"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\u2013ligand":[80],"interaction":[81],"energy,":[82],"all-atom":[83],"molecular":[84],"dynamics,":[85],"ELISA-based":[87],"CD4-binding":[88],"competition":[89,167],"assays":[90],"create,":[92],"characterize,":[93],"rationalize":[95],"models":[96],"first-":[98],"second-generation":[100],"SMCM\u2019s":[102,194,236],"bound":[103],"distinct,":[106],"trimeric":[107,186],"BG505":[108],"SOSIP.664":[109],"4NCO":[111,185],"4TVP":[113,201],"containing":[114],"with":[119,159,170,196,221,237],"no":[120],"bridging":[121],"sheet.":[122],"We":[123],"demonstrate":[124],"that":[125,183,217],"silico":[128],"neutralization":[129],"highly":[132,223],"conserved":[133,224],"D368":[134],"is":[135],"necessary":[136],"obtain":[138],"correct":[140],"orientation":[141],"their":[145],"binding":[146,166],"site":[147],"when":[148],"docking":[149,209],"against":[150],"core.":[154],"computational":[156],"results":[157],"correlate":[158],"IC":[160],"50":[161],"\u2019s":[162,173],"measured":[163,174],"ELISA":[168],"K":[171],"D":[172],"on":[175],"monomer.":[178,206],"This":[179],"supports":[180],"hypothesis":[182],"structure":[187],"represents":[188],"viable":[190],"advantages":[197],"over":[198],"both":[199],"trimer":[202],"Finally,":[207],"protocol":[210],"has":[211],"screen":[215],"compounds":[216],"can":[218],"clearly":[219],"interact":[220],"residue":[225],"D368,":[226],"increasing":[227],"likelihood":[229],"future":[231],"optimizations":[232],"arrive":[234],"at":[235],"broader":[239],"spectrum":[240],"activity.":[242]},"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":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}