{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/124433"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/124433","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"AlphaFold2 reveals structural patterns of seasonal haplotype diversification in SARS-CoV-2 structural protein variants","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2024-09-16 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2024-09-16 without embargo terms","abstract_has_math":false,"creators":["Ali, Muhammad Asif"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Bioinformatics","degree_department":null,"school":null,"contributors":["Caetano-Anollés, Gustavo","Rodriguez-Zas, Sandra L","Villamil, Maria B"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-05","date_published":"2024-05","updated_at":"2026-07-22T22:25:00Z","subjects":["Covid-19","Haplotypes","Variant Of Concern","Alphafold","Spike Protein","Mutation","Protein Structure","Evolutionary Pressure","Pandemic","Recruitment","Virus","Evolution"],"languages":["en","eng"],"rights":["Copyright 2024 Muhammad Asif Ali"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/124433","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Caetano-Anollés, Gustavo","Rodriguez-Zas, Sandra L","Villamil, Maria B"]},{"key":"dc:creator","label":"Author","values":["Ali, Muhammad Asif"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2024-05","2024-05-02"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioinformatics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Covid-19","Haplotypes","Variant Of Concern","Alphafold","Spike Protein","Mutation","Protein Structure","Evolutionary Pressure","Pandemic","Recruitment","Virus","Evolution"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2024 Muhammad Asif Ali"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/124433"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2024-09-16 without embargo terms","The student, Muhammad Ali, accepted the attached license on 2024-04-29 at 14:23.","The student, Muhammad Ali, submitted this Thesis for approval on 2024-04-29 at 15:13.","This Thesis was approved for publication on 2024-05-02 at 13:24.","DSpace SAF Submission Ingestion Package generated from Vireo submission #20694 on 2024-09-16 at 00:37:23","The COVID-19 pandemic showcases the impact of mitigation and elimination strategies across the globe, including the development of effective vaccines, antiviral drugs and diagnostic tools. However, the virus changes rapidly over time. Consequently, control strategies have been limited by time-consuming experimental acquisition of three-dimensional atomic protein structures of the fast-developing mutant ‘variants’ of the virus, which remains an unviable strategy for fast and effective disease control. Here, we use AlphaFold2 to model the atomic structure of the ever-changing SARS-CoV-2 structural proteins in silico. AlphaFold2 is an artificial intelligence (AI) deep learning computational tool capable of producing models at experimental resolution in only a few hours. Structural models for major Variants of Concern (Alpha, Delta, and Omicron) and latitude-delimited haplotypes, sets of genetically linked and highly prevalent mutations that impact the epidemic calendar of the virus, were compared to the structure of the reference Wuhan strain. We find that patterns of structural change triggered by seasonal haplotype diversification could help predict the changing face of the virus, understand seasonal behavior, and develop more resilient vaccines and drugs."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["AlphaFold2 reveals structural patterns of seasonal haplotype diversification in SARS-CoV-2 structural protein variants"]}]}],"canonical_facts":{"dc:contributor":["Caetano-Anollés, Gustavo","Rodriguez-Zas, Sandra L","Villamil, Maria B"],"dc:creator":["Ali, Muhammad Asif"],"dc:date":["2024-05","2024-05-02"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2024-09-16 without embargo terms","The student, Muhammad Ali, accepted the attached license on 2024-04-29 at 14:23.","The student, Muhammad Ali, submitted this Thesis for approval on 2024-04-29 at 15:13.","This Thesis was approved for publication on 2024-05-02 at 13:24.","DSpace SAF Submission Ingestion Package generated from Vireo submission #20694 on 2024-09-16 at 00:37:23","The COVID-19 pandemic showcases the impact of mitigation and elimination strategies across the globe, including the development of effective vaccines, antiviral drugs and diagnostic tools. However, the virus changes rapidly over time. Consequently, control strategies have been limited by time-consuming experimental acquisition of three-dimensional atomic protein structures of the fast-developing mutant ‘variants’ of the virus, which remains an unviable strategy for fast and effective disease control. Here, we use AlphaFold2 to model the atomic structure of the ever-changing SARS-CoV-2 structural proteins in silico. AlphaFold2 is an artificial intelligence (AI) deep learning computational tool capable of producing models at experimental resolution in only a few hours. Structural models for major Variants of Concern (Alpha, Delta, and Omicron) and latitude-delimited haplotypes, sets of genetically linked and highly prevalent mutations that impact the epidemic calendar of the virus, were compared to the structure of the reference Wuhan strain. We find that patterns of structural change triggered by seasonal haplotype diversification could help predict the changing face of the virus, understand seasonal behavior, and develop more resilient vaccines and drugs."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/124433"],"dc:language":["en","eng"],"dc:rights":["Copyright 2024 Muhammad Asif Ali"],"dc:subject":["Covid-19","Haplotypes","Variant Of Concern","Alphafold","Spike Protein","Mutation","Protein Structure","Evolutionary Pressure","Pandemic","Recruitment","Virus","Evolution"],"dc:title":["AlphaFold2 reveals structural patterns of seasonal haplotype diversification in SARS-CoV-2 structural protein variants"],"dc:type":["text"],"thesis:degree_discipline":["Bioinformatics"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:00Z"}