{"id":"https://openalex.org/W4385622872","doi":"https://doi.org/10.1021/acs.jcim.3c00778","title":"Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms","display_name":"Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms","publication_year":2023,"publication_date":"2023-08-07","ids":{"openalex":"https://openalex.org/W4385622872","doi":"https://doi.org/10.1021/acs.jcim.3c00778","pmid":"https://pubmed.ncbi.nlm.nih.gov/37549201"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00778","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00778","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":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11162552/pdf/nihms-1995450.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013883660","display_name":"Sian Xiao","orcid":"https://orcid.org/0000-0002-3451-5227"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sian Xiao","raw_affiliation_strings":["Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088855335","display_name":"Mohammed Alshahrani","orcid":"https://orcid.org/0009-0002-3504-6386"},"institutions":[{"id":"https://openalex.org/I185071736","display_name":"Chapman University","ror":"https://ror.org/0452jzg20","country_code":"US","type":"education","lineage":["https://openalex.org/I185071736"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammed Alshahrani","raw_affiliation_strings":["Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States"],"affiliations":[{"raw_affiliation_string":"Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States","institution_ids":["https://openalex.org/I185071736"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023698777","display_name":"Grace Gupta","orcid":null},"institutions":[{"id":"https://openalex.org/I185071736","display_name":"Chapman University","ror":"https://ror.org/0452jzg20","country_code":"US","type":"education","lineage":["https://openalex.org/I185071736"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Grace Gupta","raw_affiliation_strings":["Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States"],"affiliations":[{"raw_affiliation_string":"Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States","institution_ids":["https://openalex.org/I185071736"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010373442","display_name":"Peng Tao","orcid":"https://orcid.org/0000-0002-2488-0239"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peng Tao","raw_affiliation_strings":["Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031922505","display_name":"Gennady M. Verkhivker","orcid":"https://orcid.org/0000-0002-4507-4471"},"institutions":[{"id":"https://openalex.org/I185071736","display_name":"Chapman University","ror":"https://ror.org/0452jzg20","country_code":"US","type":"education","lineage":["https://openalex.org/I185071736"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gennady Verkhivker","raw_affiliation_strings":["Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States","Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States","institution_ids":["https://openalex.org/I185071736"]},{"raw_affiliation_string":"Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States","institution_ids":["https://openalex.org/I185071736"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5010373442","https://openalex.org/A5031922505"],"corresponding_institution_ids":["https://openalex.org/I178169726","https://openalex.org/I185071736"],"apc_list":null,"apc_paid":null,"fwci":8.0783,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.98395599,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"63","issue":"16","first_page":"5272","last_page":"5296"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9998999834060669,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11515","display_name":"Bacillus and Francisella bacterial research","score":0.9916999936103821,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.8585011959075928},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5812204480171204},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.49926114082336426},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4418167173862457},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4212774634361267},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41960012912750244},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40276575088500977},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31762075424194336},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.31011706590652466},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26875734329223633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.14712095260620117},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.08982989192008972},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07697659730911255}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.8585011959075928},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5812204480171204},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.49926114082336426},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4418167173862457},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4212774634361267},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41960012912750244},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40276575088500977},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31762075424194336},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.31011706590652466},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26875734329223633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.14712095260620117},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.08982989192008972},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07697659730911255},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003142","descriptor_name":"Communication","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":"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":"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":"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.3c00778","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00778","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:37549201","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37549201","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:digitalcommons.chapman.edu:scs_articles-2118","is_oa":true,"landing_page_url":"https://digitalcommons.chapman.edu/scs_articles/1118","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11162552/pdf/nihms-1995450.pdf","source":{"id":"https://openalex.org/S4377196324","display_name":"Chapman University Digital Commons (Chapman University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I185071736","host_organization_name":"Chapman University","host_organization_lineage":["https://openalex.org/I185071736"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Mathematics, Physics, and Computer Science Faculty Articles and Research","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11162552","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11162552","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:digitalcommons.chapman.edu:scs_articles-2118","is_oa":true,"landing_page_url":"https://digitalcommons.chapman.edu/scs_articles/1118","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11162552/pdf/nihms-1995450.pdf","source":{"id":"https://openalex.org/S4377196324","display_name":"Chapman University Digital Commons (Chapman University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I185071736","host_organization_name":"Chapman University","host_organization_lineage":["https://openalex.org/I185071736"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Mathematics, Physics, and Computer Science Faculty Articles and Research","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1488049601","display_name":null,"funder_award_id":"R15GM122013","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2884776824","display_name":null,"funder_award_id":"A20-0032","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4236183662","display_name":null,"funder_award_id":"A20-0032","funder_id":"https://openalex.org/F4320319115","funder_display_name":"Kay Family Foundation"},{"id":"https://openalex.org/G706801179","display_name":null,"funder_award_id":"R15GM122013","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8320523107","display_name":null,"funder_award_id":"GM122013","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320311541","display_name":"Chapman University","ror":"https://ror.org/0452jzg20"},{"id":"https://openalex.org/F4320319115","display_name":"Kay Family Foundation","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385622872.pdf"},"referenced_works_count":145,"referenced_works":["https://openalex.org/W165538626","https://openalex.org/W1976499671","https://openalex.org/W1981276685","https://openalex.org/W1986743126","https://openalex.org/W2001296212","https://openalex.org/W2023490488","https://openalex.org/W2031616354","https://openalex.org/W2062884696","https://openalex.org/W2066795144","https://openalex.org/W2091701505","https://openalex.org/W2093694964","https://openalex.org/W2103693942","https://openalex.org/W2106140689","https://openalex.org/W2106648157","https://openalex.org/W2150981663","https://openalex.org/W2156620408","https://openalex.org/W2157605186","https://openalex.org/W2159884214","https://openalex.org/W2167686614","https://openalex.org/W2168798454","https://openalex.org/W2170060741","https://openalex.org/W2226825552","https://openalex.org/W2315297180","https://openalex.org/W2330799739","https://openalex.org/W2344557669","https://openalex.org/W2345331290","https://openalex.org/W2397367200","https://openalex.org/W2408440099","https://openalex.org/W2411913461","https://openalex.org/W2423210081","https://openalex.org/W2469262244","https://openalex.org/W2544136853","https://openalex.org/W2555870966","https://openalex.org/W2604971487","https://openalex.org/W2616691686","https://openalex.org/W2801241269","https://openalex.org/W2807983521","https://openalex.org/W2887981960","https://openalex.org/W2911329269","https://openalex.org/W2945661338","https://openalex.org/W2949223833","https://openalex.org/W2963426504","https://openalex.org/W2981507824","https://openalex.org/W3007500173","https://openalex.org/W3007643904","https://openalex.org/W3009335299","https://openalex.org/W3011537081","https://openalex.org/W3015190630","https://openalex.org/W3019687594","https://openalex.org/W3042332408","https://openalex.org/W3044914269","https://openalex.org/W3045149055","https://openalex.org/W3046414208","https://openalex.org/W3047461618","https://openalex.org/W3048714202","https://openalex.org/W3058836816","https://openalex.org/W3087347658","https://openalex.org/W3087409770","https://openalex.org/W3089840021","https://openalex.org/W3095499424","https://openalex.org/W3097974261","https://openalex.org/W3103843063","https://openalex.org/W3108980364","https://openalex.org/W3125256861","https://openalex.org/W3125912401","https://openalex.org/W3130442532","https://openalex.org/W3138278914","https://openalex.org/W3150505176","https://openalex.org/W3157679298","https://openalex.org/W3157697503","https://openalex.org/W3162048346","https://openalex.org/W3164917922","https://openalex.org/W3168708929","https://openalex.org/W3193526107","https://openalex.org/W3195039506","https://openalex.org/W3201038556","https://openalex.org/W3208696217","https://openalex.org/W4200170677","https://openalex.org/W4205331651","https://openalex.org/W4206153788","https://openalex.org/W4206737621","https://openalex.org/W4206898072","https://openalex.org/W4210943449","https://openalex.org/W4212851383","https://openalex.org/W4213002013","https://openalex.org/W4213003635","https://openalex.org/W4213222685","https://openalex.org/W4214735462","https://openalex.org/W4220680013","https://openalex.org/W4220807057","https://openalex.org/W4220840634","https://openalex.org/W4220861013","https://openalex.org/W4220900149","https://openalex.org/W4220904663","https://openalex.org/W4221084154","https://openalex.org/W4221116249","https://openalex.org/W4223982540","https://openalex.org/W4225314443","https://openalex.org/W4225501232","https://openalex.org/W4226074646","https://openalex.org/W4226110365","https://openalex.org/W4226210265","https://openalex.org/W4226443473","https://openalex.org/W4226548601","https://openalex.org/W4281677931","https://openalex.org/W4281696741","https://openalex.org/W4281754639","https://openalex.org/W4281873659","https://openalex.org/W4282555588","https://openalex.org/W4282939988","https://openalex.org/W4282982164","https://openalex.org/W4283026725","https://openalex.org/W4283380375","https://openalex.org/W4283646162","https://openalex.org/W4285009335","https://openalex.org/W4286220782","https://openalex.org/W4292883071","https://openalex.org/W4295777530","https://openalex.org/W4298325528","https://openalex.org/W4301394219","https://openalex.org/W4306740332","https://openalex.org/W4308497376","https://openalex.org/W4309306331","https://openalex.org/W4309469480","https://openalex.org/W4309686974","https://openalex.org/W4311359167","https://openalex.org/W4311495385","https://openalex.org/W4311664557","https://openalex.org/W4312019047","https://openalex.org/W4312045153","https://openalex.org/W4313887879","https://openalex.org/W4317771836","https://openalex.org/W4317886130","https://openalex.org/W4318065436","https://openalex.org/W4319066889","https://openalex.org/W4319455345","https://openalex.org/W4320341731","https://openalex.org/W4320728217","https://openalex.org/W4324380305","https://openalex.org/W4362580966","https://openalex.org/W4367174467","https://openalex.org/W4367838604","https://openalex.org/W4376223660","https://openalex.org/W4376872235","https://openalex.org/W4378516469"],"related_works":["https://openalex.org/W2939998722","https://openalex.org/W2169750653","https://openalex.org/W2195592873","https://openalex.org/W1971782741","https://openalex.org/W3005062988","https://openalex.org/W2075777827","https://openalex.org/W4211217675","https://openalex.org/W2592466923","https://openalex.org/W1555254413","https://openalex.org/W4231759675"],"abstract_inverted_index":{"The":[0,138],"new":[1],"generation":[2],"of":[3,34,62,94,105,134,144,153,178,197,205,211,216,237,242],"SARS-CoV-2":[4,35,64,159],"Omicron":[5,83,124],"variants":[6],"displayed":[7],"a":[8,91],"significant":[9],"growth":[10],"advantage":[11],"and":[12,49,57,81,87,99,117,131,185,203,214,226,235],"increased":[13,102],"viral":[14],"fitness":[15],"by":[16],"acquiring":[17],"convergent":[18,27,168,198,229],"mutations,":[19],"suggesting":[20],"that":[21,141,228],"the":[22,31,38,63,68,73,95,101,106,135,145,149,154,158,246],"immune":[23,179],"pressure":[24],"can":[25,110,126,162],"promote":[26],"evolution":[28,234],"leading":[29],"to":[30,53,113],"sudden":[32],"acceleration":[33],"evolution.":[36],"In":[37],"current":[39],"study,":[40],"we":[41,192],"combined":[42],"structural":[43,122],"modeling,":[44],"microsecond":[45],"molecular":[46],"dynamics":[47],"simulations,":[48],"Markov":[50],"state":[51],"models":[52],"characterize":[54],"conformational":[55,97,136,146,212,243],"landscapes":[56],"identify":[58],"specific":[59,132],"dynamic":[60,115,129],"signatures":[61,130],"spike":[65,160],"complexes":[66],"with":[67,189],"host":[69],"receptor":[70],"ACE2":[71],"for":[72,176],"recently":[74],"emerged":[75],"highly":[76],"transmissible":[77],"XBB.1,":[78],"XBB.1.5,":[79],"BQ.1,":[80],"BQ.1.1":[82,118],"variants.":[84],"Microsecond":[85],"simulations":[86,184],"Markovian":[88,186],"modeling":[89,187],"provided":[90],"detailed":[92],"characterization":[93],"functional":[96,150],"states":[98],"revealed":[100,222],"thermodynamic":[103],"stabilization":[104],"XBB.1.5":[107],"subvariant,":[108],"which":[109,170],"be":[111,163],"contrasted":[112],"more":[114],"BQ.1":[116],"subvariants.":[119],"Despite":[120],"considerable":[121],"similarities,":[123],"mutations":[125,169],"induce":[127],"unique":[128],"distributions":[133],"states.":[137],"results":[139],"suggested":[140,227],"variant-specific":[142],"changes":[143],"mobility":[147],"in":[148,157,209,245],"interfacial":[151],"loops":[152],"receptor-binding":[155],"domain":[156],"protein":[161],"fine-tuned":[164],"through":[165,240],"crosstalk":[166],"between":[167],"could":[171,232],"provide":[172],"an":[173],"evolutionary":[174],"path":[175],"modulation":[177,210,241],"escape.":[180],"By":[181],"combining":[182],"atomistic":[183],"analysis":[188],"perturbation-based":[190],"approaches,":[191],"determined":[193],"important":[194],"complementary":[195],"roles":[196],"mutation":[199,230],"sites":[200,231],"as":[201],"effectors":[202],"receivers":[204],"allosteric":[206,217,224,238],"signaling":[207],"involved":[208],"plasticity":[213,244],"regulation":[215],"communications.":[218],"This":[219],"study":[220],"also":[221],"hidden":[223],"pockets":[225,239],"control":[233],"distribution":[236],"flexible":[247],"adaptable":[248],"regions.":[249]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":6}],"updated_date":"2026-04-12T07:58:50.170612","created_date":"2025-10-10T00:00:00"}