{"id":"https://openalex.org/W2092887868","doi":"https://doi.org/10.1371/journal.pcbi.1003046","title":"A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein","display_name":"A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein","publication_year":2013,"publication_date":"2013-05-16","ids":{"openalex":"https://openalex.org/W2092887868","doi":"https://doi.org/10.1371/journal.pcbi.1003046","mag":"2092887868","pmid":"https://pubmed.ncbi.nlm.nih.gov/23696718"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003046","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003046","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003046&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003046&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085693193","display_name":"Anurag Sethi","orcid":"https://orcid.org/0000-0003-3295-3116"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anurag Sethi","raw_affiliation_strings":["Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA","Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100921080","display_name":"Tian Jianhui","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianhui Tian","raw_affiliation_strings":["Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America,","Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America,","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026220972","display_name":"Cynthia A. Derdeyn","orcid":"https://orcid.org/0000-0002-1220-513X"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cynthia A. Derdeyn","raw_affiliation_strings":["Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America","Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America","Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America"],"affiliations":[{"raw_affiliation_string":"Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022985881","display_name":"Bette Korber","orcid":"https://orcid.org/0000-0002-2026-5757"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bette Korber","raw_affiliation_strings":["Center for HIV/AIDS Vaccine Immunology, School of Medicine, Duke University, Durham, North Carolina, United States of America","Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America,","Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for HIV/AIDS Vaccine Immunology, School of Medicine, Duke University, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America,","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037917270","display_name":"S. Gnanakaran","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S. Gnanakaran","raw_affiliation_strings":["Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America,","Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America,","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5037917270"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.8567,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.85468515,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9","issue":"5","first_page":"e1003046","last_page":"e1003046"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998000264167786,"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":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9955000281333923,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9715999960899353,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/gp41","display_name":"Gp41","score":0.7168328762054443},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6002359390258789},{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.5586764216423035},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5253186225891113},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4832202196121216},{"id":"https://openalex.org/keywords/immunogen","display_name":"Immunogen","score":0.4461468756198883},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.394405722618103},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3405618667602539},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.2011067271232605},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.1181144118309021}],"concepts":[{"id":"https://openalex.org/C2776258796","wikidata":"https://www.wikidata.org/wiki/Q5590520","display_name":"Gp41","level":4,"score":0.7168328762054443},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6002359390258789},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.5586764216423035},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5253186225891113},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4832202196121216},{"id":"https://openalex.org/C2779909307","wikidata":"https://www.wikidata.org/wiki/Q1660181","display_name":"Immunogen","level":4,"score":0.4461468756198883},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.394405722618103},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3405618667602539},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.2011067271232605},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.1181144118309021},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015699","descriptor_name":"HIV Envelope Protein gp120","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015704","descriptor_name":"CD4 Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","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},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1003046","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003046","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003046&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:23696718","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23696718","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:osti.gov:1627230","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1627230","pdf_url":"https://www.osti.gov/servlets/purl/1627230","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.787.9179","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.787.9179","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/01/2c/pcbi.1003046.PMC3656115.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:880186ee833746e08d387f48f4f57d7b","is_oa":true,"landing_page_url":"https://doaj.org/article/880186ee833746e08d387f48f4f57d7b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 9, Iss 5, p e1003046 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2656197","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3656115","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/704185","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_A_Mechanistic_Understanding_of_Allosteric_Immune_Escape_Pathways_in_the_HIV_1_Envelope_Glycoprotein_/704185","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003046","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003046","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003046&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1835569409","display_name":null,"funder_award_id":"AI100645","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2063224830","display_name":null,"funder_award_id":"AI067854","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2688119162","display_name":null,"funder_award_id":"P01AI088610","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3833313268","display_name":null,"funder_award_id":"AI100645","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4437485056","display_name":null,"funder_award_id":"AI067854","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5854700120","display_name":null,"funder_award_id":"AI088610","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5903061775","display_name":null,"funder_award_id":"NIAID","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8321809729","display_name":null,"funder_award_id":"U19-AI067854","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8994518985","display_name":null,"funder_award_id":"AI067854-07","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2092887868.pdf","grobid_xml":"https://content.openalex.org/works/W2092887868.grobid-xml"},"referenced_works_count":113,"referenced_works":["https://openalex.org/W196933227","https://openalex.org/W1607931568","https://openalex.org/W1794879226","https://openalex.org/W1871986172","https://openalex.org/W1966770601","https://openalex.org/W1968872901","https://openalex.org/W1971421925","https://openalex.org/W1974033269","https://openalex.org/W1977482735","https://openalex.org/W1982403911","https://openalex.org/W1982874561","https://openalex.org/W1986159600","https://openalex.org/W1989468850","https://openalex.org/W1990374415","https://openalex.org/W1991764480","https://openalex.org/W1992566288","https://openalex.org/W1996011751","https://openalex.org/W1996765646","https://openalex.org/W1997677784","https://openalex.org/W1997989849","https://openalex.org/W1998412941","https://openalex.org/W2000483448","https://openalex.org/W2000925655","https://openalex.org/W2003302807","https://openalex.org/W2004669329","https://openalex.org/W2005099669","https://openalex.org/W2005780220","https://openalex.org/W2007249947","https://openalex.org/W2009123297","https://openalex.org/W2011168681","https://openalex.org/W2011669324","https://openalex.org/W2012057091","https://openalex.org/W2012510847","https://openalex.org/W2013234834","https://openalex.org/W2016582810","https://openalex.org/W2017149825","https://openalex.org/W2017551575","https://openalex.org/W2020426074","https://openalex.org/W2020596573","https://openalex.org/W2025005245","https://openalex.org/W2027309027","https://openalex.org/W2027408247","https://openalex.org/W2029856966","https://openalex.org/W2034587047","https://openalex.org/W2035864527","https://openalex.org/W2036919909","https://openalex.org/W2039363610","https://openalex.org/W2049598343","https://openalex.org/W2049661341","https://openalex.org/W2051893115","https://openalex.org/W2058416188","https://openalex.org/W2060079863","https://openalex.org/W2062204035","https://openalex.org/W2064703363","https://openalex.org/W2066926304","https://openalex.org/W2067080638","https://openalex.org/W2067174909","https://openalex.org/W2072973641","https://openalex.org/W2080089116","https://openalex.org/W2081291921","https://openalex.org/W2083975423","https://openalex.org/W2085166312","https://openalex.org/W2087284052","https://openalex.org/W2089135598","https://openalex.org/W2090264443","https://openalex.org/W2092417121","https://openalex.org/W2096346675","https://openalex.org/W2096598657","https://openalex.org/W2098439468","https://openalex.org/W2098781795","https://openalex.org/W2099904971","https://openalex.org/W2101244907","https://openalex.org/W2102254707","https://openalex.org/W2102503844","https://openalex.org/W2102670802","https://openalex.org/W2103388411","https://openalex.org/W2103945336","https://openalex.org/W2105041993","https://openalex.org/W2111488694","https://openalex.org/W2111914135","https://openalex.org/W2113282092","https://openalex.org/W2115152262","https://openalex.org/W2118274231","https://openalex.org/W2118474642","https://openalex.org/W2120031187","https://openalex.org/W2122617162","https://openalex.org/W2122909018","https://openalex.org/W2128579789","https://openalex.org/W2130582243","https://openalex.org/W2133233128","https://openalex.org/W2136665045","https://openalex.org/W2141666704","https://openalex.org/W2142595184","https://openalex.org/W2143421242","https://openalex.org/W2144391203","https://openalex.org/W2144413761","https://openalex.org/W2144539981","https://openalex.org/W2145525301","https://openalex.org/W2145909184","https://openalex.org/W2147009832","https://openalex.org/W2149744037","https://openalex.org/W2150981663","https://openalex.org/W2151739788","https://openalex.org/W2153163225","https://openalex.org/W2157615131","https://openalex.org/W2158666214","https://openalex.org/W2160329145","https://openalex.org/W2883755802","https://openalex.org/W3012535303","https://openalex.org/W3037896947","https://openalex.org/W3106205370","https://openalex.org/W4211232835","https://openalex.org/W6607973293"],"related_works":["https://openalex.org/W2393764744","https://openalex.org/W2008317712","https://openalex.org/W2417982011","https://openalex.org/W2388008635","https://openalex.org/W3137182620","https://openalex.org/W3210061095","https://openalex.org/W3030069513","https://openalex.org/W625192361","https://openalex.org/W2029057270","https://openalex.org/W1991572753"],"abstract_inverted_index":{"The":[0,169],"HIV-1":[1,30,93,246],"envelope":[2],"(Env)":[3],"spike,":[4],"which":[5],"consists":[6],"of":[7,12,21,29,33,64,111,120,134,141,177,189,220],"a":[8,79,117,204,232],"compact,":[9],"heterodimeric":[10],"trimer":[11],"the":[13,19,25,49,60,131,135,139,145,157,166,178,187,195,211,218],"glycoproteins":[14],"gp120":[15,95,136,167,193],"and":[16,31,73,103,107,159,163,174],"gp41,":[17],"is":[18,200],"target":[20],"neutralizing":[22,39,257],"antibodies.":[23],"However,":[24],"high":[26,118],"mutation":[27],"rate":[28],"plasticity":[32],"Env":[34,94,254],"facilitates":[35],"viral":[36],"evasion":[37,88],"from":[38,48,98],"antibodies":[40],"through":[41],"various":[42],"mechanisms.":[43],"Mutations":[44],"that":[45,124,185,245,255],"are":[46,69],"distant":[47,128],"antibody":[50,251,258],"binding":[51],"site":[52],"can":[53],"lead":[54],"to":[55,71,83,248],"escape,":[56],"probably":[57],"by":[58,148],"changing":[59],"conformation":[61],"or":[62],"dynamics":[63,113,133],"Env;":[65],"however,":[66],"these":[67,224],"changes":[68],"difficult":[70],"identify":[72,84],"define":[74],"mechanistically.":[75],"Here":[76],"we":[77,155],"describe":[78],"network":[80,153],"analysis-based":[81],"approach":[82],"potential":[85],"allosteric":[86],"immune":[87],"mechanisms":[89],"using":[90],"three":[91,190],"known":[92],"protein":[96],"structures":[97],"two":[99],"different":[100],"clades,":[101],"B":[102],"C.":[104],"First,":[105],"correlation":[106],"principal":[108],"component":[109],"analyses":[110],"molecular":[112],"(MD)":[114],"simulations":[115,151],"identified":[116,156],"degree":[119],"long-distance":[121,142],"coupled":[122],"motions":[123],"exist":[125],"between":[126],"functionally":[127],"regions":[129],"within":[130,165,186,223],"intrinsic":[132],"core,":[137],"supporting":[138],"presence":[140],"communication":[143,161,179,199,225],"in":[144,181,207,214,253],"protein.":[146],"Then,":[147],"integrating":[149],"MD":[150],"with":[152],"theory,":[154],"optimal":[158,196,212],"suboptimal":[160,205],"pathways":[162,180],"modules":[164],"core.":[168],"results":[170],"unveil":[171],"both":[172],"strain-dependent":[173],"-independent":[175],"characteristics":[176],"gp120.":[182],"We":[183],"show":[184],"context":[188],"structurally":[191],"homologous":[192],"cores,":[194],"pathway":[197,206,213],"for":[198,235],"sequence":[201],"sensitive,":[202],"i.e.":[203],"one":[208],"strain":[209],"becomes":[210],"another":[215],"strain.":[216],"Yet":[217],"identification":[219],"conserved":[221],"elements":[222],"pathways,":[226],"termed":[227],"inter-modular":[228],"hotspots,":[229],"could":[230,240],"present":[231],"new":[233],"opportunity":[234],"immunogen":[236],"design,":[237],"as":[238],"this":[239],"be":[241],"an":[242],"additional":[243],"mechanism":[244],"uses":[247],"shield":[249],"vulnerable":[250],"targets":[252],"induce":[256],"breadth.":[259]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}