{"id":"https://openalex.org/W4412203396","doi":"https://doi.org/10.1021/acs.jcim.5c00308","title":"Conformational Dynamics and Binding Interactions of SARS-CoV-2 Spike Protein Variants: Omicron, XBB.1.9.2, and EG.5","display_name":"Conformational Dynamics and Binding Interactions of SARS-CoV-2 Spike Protein Variants: Omicron, XBB.1.9.2, and EG.5","publication_year":2025,"publication_date":"2025-07-11","ids":{"openalex":"https://openalex.org/W4412203396","doi":"https://doi.org/10.1021/acs.jcim.5c00308","pmid":"https://pubmed.ncbi.nlm.nih.gov/40643983"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00308","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00308","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.5c00308","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088169401","display_name":"Clauber Henrique Souza da Costa","orcid":"https://orcid.org/0000-0002-6915-1056"},"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"]},{"id":"https://openalex.org/I4210143490","display_name":"Computing Center","ror":"https://ror.org/0557kgc34","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210143490","https://openalex.org/I4210148470"]}],"countries":["BR","RU"],"is_corresponding":true,"raw_author_name":"Clauber Henrique Souza da Costa","raw_affiliation_strings":["Institute of Chemistry and Center for Computing in Engineering & Sciences","University of Campinas \u2212 UNICAMP"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Chemistry and Center for Computing in Engineering & Sciences","institution_ids":["https://openalex.org/I4210143490"]},{"raw_affiliation_string":"University of Campinas \u2212 UNICAMP","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057123138","display_name":"Camila Auad Beltr\u00e3o de Freitas","orcid":"https://orcid.org/0000-0003-1765-7925"},"institutions":[{"id":"https://openalex.org/I59606676","display_name":"Universidade Federal do Par\u00e1","ror":"https://ror.org/03q9sr818","country_code":"BR","type":"education","lineage":["https://openalex.org/I59606676"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Camila Auad Beltr\u00e3o de Freitas","raw_affiliation_strings":["Laborat\u00f3rio de Planejamento e Desenvolvimento de F\u00e1rmacos, Instituto de Ci\u00eancias Exatas e Naturais","Universidade Federal do Par\u00e1"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Planejamento e Desenvolvimento de F\u00e1rmacos, Instituto de Ci\u00eancias Exatas e Naturais","institution_ids":[]},{"raw_affiliation_string":"Universidade Federal do Par\u00e1","institution_ids":["https://openalex.org/I59606676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028159090","display_name":"Alberto Santos","orcid":"https://orcid.org/0000-0002-7033-3922"},"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"]},{"id":"https://openalex.org/I4210143490","display_name":"Computing Center","ror":"https://ror.org/0557kgc34","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210143490","https://openalex.org/I4210148470"]}],"countries":["BR","RU"],"is_corresponding":false,"raw_author_name":"Alberto Monteiro dos Santos","raw_affiliation_strings":["Institute of Chemistry and Center for Computing in Engineering & Sciences","University of Campinas \u2212 UNICAMP"],"raw_orcid":"https://orcid.org/0000-0002-7033-3922","affiliations":[{"raw_affiliation_string":"Institute of Chemistry and Center for Computing in Engineering & Sciences","institution_ids":["https://openalex.org/I4210143490"]},{"raw_affiliation_string":"University of Campinas \u2212 UNICAMP","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104278529","display_name":"Carlos Gabriel da Silva de Souza","orcid":"https://orcid.org/0000-0001-6572-7196"},"institutions":[{"id":"https://openalex.org/I59606676","display_name":"Universidade Federal do Par\u00e1","ror":"https://ror.org/03q9sr818","country_code":"BR","type":"education","lineage":["https://openalex.org/I59606676"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Carlos Gabriel da Silva de Souza","raw_affiliation_strings":["Laborat\u00f3rio de Planejamento e Desenvolvimento de F\u00e1rmacos, Instituto de Ci\u00eancias Exatas e Naturais","Universidade Federal do Par\u00e1"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Planejamento e Desenvolvimento de F\u00e1rmacos, Instituto de Ci\u00eancias Exatas e Naturais","institution_ids":[]},{"raw_affiliation_string":"Universidade Federal do Par\u00e1","institution_ids":["https://openalex.org/I59606676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053248481","display_name":"Jos\u00e9 Rog\u00e9rio A. Silva","orcid":"https://orcid.org/0000-0003-2310-5107"},"institutions":[{"id":"https://openalex.org/I4210101325","display_name":"LungLife AI (United States)","ror":"https://ror.org/01ecs7r71","country_code":"US","type":"company","lineage":["https://openalex.org/I4210101325"]},{"id":"https://openalex.org/I4210105641","display_name":"Peptide Protein Research (United Kingdom)","ror":"https://ror.org/01e8xap89","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210105641"]},{"id":"https://openalex.org/I59606676","display_name":"Universidade Federal do Par\u00e1","ror":"https://ror.org/03q9sr818","country_code":"BR","type":"education","lineage":["https://openalex.org/I59606676"]},{"id":"https://openalex.org/I95023434","display_name":"University of KwaZulu-Natal","ror":"https://ror.org/04qzfn040","country_code":"ZA","type":"education","lineage":["https://openalex.org/I95023434"]}],"countries":["BR","GB","US","ZA"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Rog\u00e9rio A. Silva","raw_affiliation_strings":["Catalysis and Peptide Research Unit","Federal University of Par\u00e1","Laboratory of Computer Modeling of Molecular Biosystems (CompMBio)","University of KwaZulu-Natal"],"raw_orcid":"https://orcid.org/0000-0003-2310-5107","affiliations":[{"raw_affiliation_string":"Catalysis and Peptide Research Unit","institution_ids":["https://openalex.org/I4210105641"]},{"raw_affiliation_string":"Federal University of Par\u00e1","institution_ids":["https://openalex.org/I59606676"]},{"raw_affiliation_string":"Laboratory of Computer Modeling of Molecular Biosystems (CompMBio)","institution_ids":["https://openalex.org/I4210101325"]},{"raw_affiliation_string":"University of KwaZulu-Natal","institution_ids":["https://openalex.org/I95023434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087137334","display_name":"Jer\u00f4nimo Lameira","orcid":"https://orcid.org/0000-0001-7270-1517"},"institutions":[{"id":"https://openalex.org/I4210101325","display_name":"LungLife AI (United States)","ror":"https://ror.org/01ecs7r71","country_code":"US","type":"company","lineage":["https://openalex.org/I4210101325"]},{"id":"https://openalex.org/I59606676","display_name":"Universidade Federal do Par\u00e1","ror":"https://ror.org/03q9sr818","country_code":"BR","type":"education","lineage":["https://openalex.org/I59606676"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"Jer\u00f4nimo Lameira","raw_affiliation_strings":["Federal University of Par\u00e1","Laboratory of Computer Modeling of Molecular Biosystems (CompMBio)","Laborat\u00f3rio de Planejamento e Desenvolvimento de F\u00e1rmacos, Instituto de Ci\u00eancias Exatas e Naturais","Universidade Federal do Par\u00e1"],"raw_orcid":"https://orcid.org/0000-0001-7270-1517","affiliations":[{"raw_affiliation_string":"Federal University of Par\u00e1","institution_ids":["https://openalex.org/I59606676"]},{"raw_affiliation_string":"Laboratory of Computer Modeling of Molecular Biosystems (CompMBio)","institution_ids":["https://openalex.org/I4210101325"]},{"raw_affiliation_string":"Laborat\u00f3rio de Planejamento e Desenvolvimento de F\u00e1rmacos, Instituto de Ci\u00eancias Exatas e Naturais","institution_ids":[]},{"raw_affiliation_string":"Universidade Federal do Par\u00e1","institution_ids":["https://openalex.org/I59606676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002277303","display_name":"Vicent Moliner","orcid":"https://orcid.org/0000-0002-3665-3391"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Vicent Moliner","raw_affiliation_strings":["Institute of Advanced Materials (INAM)","Universitat Jaume I"],"raw_orcid":"https://orcid.org/0000-0002-3665-3391","affiliations":[{"raw_affiliation_string":"Institute of Advanced Materials (INAM)","institution_ids":[]},{"raw_affiliation_string":"Universitat Jaume I","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072069815","display_name":"Munir S. Skaf","orcid":"https://orcid.org/0000-0001-7485-1228"},"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"]},{"id":"https://openalex.org/I4210143490","display_name":"Computing Center","ror":"https://ror.org/0557kgc34","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210143490","https://openalex.org/I4210148470"]}],"countries":["BR","RU"],"is_corresponding":false,"raw_author_name":"Munir S. Skaf","raw_affiliation_strings":["Institute of Chemistry and Center for Computing in Engineering & Sciences","University of Campinas \u2212 UNICAMP"],"raw_orcid":"https://orcid.org/0000-0001-7485-1228","affiliations":[{"raw_affiliation_string":"Institute of Chemistry and Center for Computing in Engineering & Sciences","institution_ids":["https://openalex.org/I4210143490"]},{"raw_affiliation_string":"University of Campinas \u2212 UNICAMP","institution_ids":["https://openalex.org/I181391015"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5088169401"],"corresponding_institution_ids":["https://openalex.org/I181391015","https://openalex.org/I4210143490"],"apc_list":null,"apc_paid":null,"fwci":2.6514,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.91038878,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"65","issue":"14","first_page":"7651","last_page":"7667"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9973999857902527,"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":0.9973999857902527,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9927999973297119,"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/spike-protein","display_name":"Spike Protein","score":0.7352601289749146},{"id":"https://openalex.org/keywords/spike","display_name":"Spike (software development)","score":0.6173776984214783},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.596779465675354},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5494500994682312},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.5304305553436279},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4789060354232788},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4748395085334778},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43161529302597046},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2755510210990906},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.19846343994140625},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.17705297470092773},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1389668881893158},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13454976677894592}],"concepts":[{"id":"https://openalex.org/C2909509916","wikidata":"https://www.wikidata.org/wiki/Q22329850","display_name":"Spike Protein","level":5,"score":0.7352601289749146},{"id":"https://openalex.org/C2781390188","wikidata":"https://www.wikidata.org/wiki/Q25203449","display_name":"Spike (software development)","level":2,"score":0.6173776984214783},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.596779465675354},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5494500994682312},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.5304305553436279},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4789060354232788},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4748395085334778},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43161529302597046},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2755510210990906},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19846343994140625},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.17705297470092773},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1389668881893158},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13454976677894592},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.0},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c00308","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00308","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40643983","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40643983","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:pubmedcentral.nih.gov:12308811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12308811","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00308","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00308","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G1280126730","display_name":null,"funder_award_id":"CIPROM/2021/079","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"},{"id":"https://openalex.org/G1790695379","display_name":null,"funder_award_id":"2023/13707-7","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G1924486535","display_name":null,"funder_award_id":"440053/2022-6","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G3015624356","display_name":null,"funder_award_id":"2022/04695-2","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G4022475470","display_name":null,"funder_award_id":"402141/2023-7","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G5466870036","display_name":null,"funder_award_id":"443533/2024-5","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G6054263959","display_name":null,"funder_award_id":"2022/04703-5","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G6478648318","display_name":null,"funder_award_id":"PGC2018-094852-B-C21","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7148057268","display_name":null,"funder_award_id":"305182/2021-8","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G813268187","display_name":null,"funder_award_id":"304610/2023-2","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G8974603849","display_name":null,"funder_award_id":"2013/08293-7","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321864","display_name":"Generalitat Valenciana","ror":"https://ror.org/0097mvx21"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":107,"referenced_works":["https://openalex.org/W1514997862","https://openalex.org/W1558188591","https://openalex.org/W1625910593","https://openalex.org/W1969130197","https://openalex.org/W1970973025","https://openalex.org/W1975580333","https://openalex.org/W1975734016","https://openalex.org/W1976499671","https://openalex.org/W1982533785","https://openalex.org/W1985037445","https://openalex.org/W1986240377","https://openalex.org/W1992899488","https://openalex.org/W2005313434","https://openalex.org/W2016111085","https://openalex.org/W2025116694","https://openalex.org/W2071794983","https://openalex.org/W2093407764","https://openalex.org/W2096599403","https://openalex.org/W2100561975","https://openalex.org/W2141510323","https://openalex.org/W2142868265","https://openalex.org/W2144550311","https://openalex.org/W2148893085","https://openalex.org/W2151020862","https://openalex.org/W2153387948","https://openalex.org/W2159367911","https://openalex.org/W2161134038","https://openalex.org/W2171755502","https://openalex.org/W2321484219","https://openalex.org/W2327581403","https://openalex.org/W2332712348","https://openalex.org/W2335200606","https://openalex.org/W2404280981","https://openalex.org/W2510475640","https://openalex.org/W2627044601","https://openalex.org/W2901511678","https://openalex.org/W2916487223","https://openalex.org/W2952045272","https://openalex.org/W2964442101","https://openalex.org/W2992752586","https://openalex.org/W3001118548","https://openalex.org/W3005079553","https://openalex.org/W3006645647","https://openalex.org/W3011913947","https://openalex.org/W3012189167","https://openalex.org/W3014067025","https://openalex.org/W3016271240","https://openalex.org/W3016885747","https://openalex.org/W3024835017","https://openalex.org/W3034957370","https://openalex.org/W3086125063","https://openalex.org/W3092403777","https://openalex.org/W3113189927","https://openalex.org/W3116974416","https://openalex.org/W3133757194","https://openalex.org/W3136240492","https://openalex.org/W3165205080","https://openalex.org/W3180063515","https://openalex.org/W3182696180","https://openalex.org/W3193616127","https://openalex.org/W3201784646","https://openalex.org/W3203433659","https://openalex.org/W3203735717","https://openalex.org/W3215827060","https://openalex.org/W3216623344","https://openalex.org/W4200048770","https://openalex.org/W4200469371","https://openalex.org/W4205331651","https://openalex.org/W4206153788","https://openalex.org/W4206737621","https://openalex.org/W4221116249","https://openalex.org/W4280645247","https://openalex.org/W4283024935","https://openalex.org/W4289884217","https://openalex.org/W4292326316","https://openalex.org/W4295679050","https://openalex.org/W4308972771","https://openalex.org/W4311359167","https://openalex.org/W4317212025","https://openalex.org/W4317433265","https://openalex.org/W4318065436","https://openalex.org/W4319066889","https://openalex.org/W4323363071","https://openalex.org/W4376872235","https://openalex.org/W4382983551","https://openalex.org/W4385620012","https://openalex.org/W4385987038","https://openalex.org/W4386162732","https://openalex.org/W4386256230","https://openalex.org/W4386594932","https://openalex.org/W4386618217","https://openalex.org/W4386700314","https://openalex.org/W4386724915","https://openalex.org/W4387849815","https://openalex.org/W4388897344","https://openalex.org/W4389819431","https://openalex.org/W4389952097","https://openalex.org/W4390038031","https://openalex.org/W4390732981","https://openalex.org/W4391934251","https://openalex.org/W4392761745","https://openalex.org/W4393971152","https://openalex.org/W4396606103","https://openalex.org/W4401613332","https://openalex.org/W4402520598","https://openalex.org/W4406155765","https://openalex.org/W6922541683"],"related_works":["https://openalex.org/W3135501652","https://openalex.org/W3207585454","https://openalex.org/W4394761436","https://openalex.org/W4243078506","https://openalex.org/W4372292428","https://openalex.org/W3017562527","https://openalex.org/W3121068275","https://openalex.org/W4386864284","https://openalex.org/W4205815969","https://openalex.org/W3023726384"],"abstract_inverted_index":{"The":[0,21,165,202,219],"SARS-CoV-2":[1,25,133],"virus,":[2],"responsible":[3],"for":[4,81,94,232,239],"the":[5,33,37,42,63,68,73,86,116,121,125,141,152,157,160,176,195,213],"COVID-19":[6,257],"pandemic,":[7],"has":[8,47],"continuously":[9],"evolved,":[10],"generating":[11],"numerous":[12],"variants":[13,170],"with":[14,179,205],"varying":[15],"degrees":[16],"of":[17,24,32,36,62,159],"infectivity":[18],"and":[19,56,110,124,134,140,168,193,247,258],"transmissibility.":[20,58],"EG.5":[22,46,66,143,169,203,223],"subvariant":[23],"emerged":[26],"globally":[27],"in":[28,72,131,222],"mid-2023":[29],"as":[30],"part":[31],"ongoing":[34,214],"evolution":[35],"Omicron":[38],"lineage.":[39],"Derived":[40],"from":[41],"recombinant":[43],"XBB.1.9":[44],"sublineage,":[45],"attracted":[48],"attention":[49],"due":[50],"to":[51,114,210,254],"its":[52,135,206,229,259],"enhanced":[53],"immune":[54],"escape":[55],"sustained":[57],"As":[59],"a":[60,78],"member":[61],"FLip":[64],"lineage,":[65],"harbors":[67],"convergent":[69],"F456L":[70,220],"mutation":[71,221],"spike":[74,122,162],"receptor-binding":[75],"domain":[76],"(RBD),":[77],"key":[79,182],"residue":[80],"neutralizing":[82],"antibody":[83],"recognition.":[84],"Understanding":[85],"molecular":[87,105,118],"mechanisms":[88],"underlying":[89],"these":[90],"variations":[91],"is":[92,252],"crucial":[93],"developing":[95],"effective":[96],"antiviral":[97,242],"strategies.":[98],"In":[99],"this":[100],"study,":[101],"we":[102],"employed":[103],"accelerated":[104],"dynamics":[106],"simulations,":[107],"free-energy":[108],"calculations,":[109],"interaction":[111],"fingerprint":[112],"analysis,":[113],"investigate":[115],"intricate":[117],"interactions":[119,150],"between":[120],"RBD":[123],"angiotensin-converting":[126],"enzyme":[127],"2":[128],"(ACE2)":[129],"receptor":[130],"wild-type":[132],"variants,":[136],"specifically":[137],"Omicron,":[138,166],"XBB.1.9.2,":[139,167],"concerning":[142],"variant.":[144],"Our":[145,234],"findings":[146],"reveal":[147],"that":[148],"electrostatic":[149,173,200],"are":[151],"predominant":[153],"driving":[154],"force":[155],"behind":[156],"stabilization":[158],"viral":[161],"protein-ACE2":[163],"complex.":[164],"exhibit":[171],"distinct":[172],"profiles":[174],"at":[175,181],"spike-ACE2":[177,196],"interface,":[178],"mutations":[180],"residues":[183],"reconfiguring":[184],"local":[185],"interactions.":[186,201],"These":[187],"changes":[188],"enhance":[189],"ACE2":[190],"binding":[191,208],"specificity":[192],"stabilize":[194],"complex":[197],"through":[198],"intensified":[199],"variant,":[204],"stronger":[207],"affinity":[209,231],"ACE2,":[211],"underscores":[212],"threat":[215],"posed":[216],"by":[217],"SARS-CoV-2.":[218],"enhances":[224],"protein":[225],"stability,":[226],"further":[227],"supporting":[228],"increased":[230],"ACE2.":[233],"research":[235,251],"provides":[236],"valuable":[237],"insights":[238],"designing":[240],"targeted":[241],"therapies,":[243],"including":[244],"peptide":[245],"inhibitors":[246],"bioactive":[248],"compounds.":[249],"Continuous":[250],"essential":[253],"effectively":[255],"combat":[256],"evolving":[260],"variants.":[261]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
