{"id":"W4379930681","doi":"10.2196/43906","title":"Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis","year":2023,"lang":"en","type":"article","venue":"JMIR Bioinformatics and Biotechnology","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Nonsynonymous substitution; Phylogenetic tree; Biology; Mega-; Sequence analysis; Mutation; Pandemic; Genetics; Virology; Multiple sequence alignment; Sequence alignment; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); GenBank; Amino acid residue; Computational biology; Gene; Peptide sequence; Coronavirus disease 2019 (COVID-19); Disease; Genome; Medicine; Infectious disease (medical specialty)","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004982716,0.0001996624,0.0004719177,0.001583864,0.0001342931,0.00005828697,0.0002661833,0.0003812573,0.000002230506],"category_scores_gemma":[0.0001382951,0.0001300223,0.00009772787,0.003064198,0.0005553987,0.0001875431,0.0002034544,0.0004060089,0.0000154869],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002783623,"about_ca_system_score_gemma":0.00009966044,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001788815,"about_ca_topic_score_gemma":0.0002421416,"domain_scores_codex":[0.9983583,0.00002782248,0.0007129053,0.0001615548,0.0003367755,0.0004026198],"domain_scores_gemma":[0.9990767,0.0001172503,0.0002069959,0.0004818585,0.00009428244,0.00002292081],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0008839656,0.0008104361,0.1971349,0.00824253,0.005049484,0.0004131808,0.05764985,0.00002431187,0.2185508,0.05149012,0.002955532,0.4567949],"study_design_scores_gemma":[0.005461857,0.001906702,0.1267891,0.0002332645,0.0009022647,0.0004984452,0.01878877,0.6644284,0.1613208,0.00366899,0.01521468,0.0007867719],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.994804,0.00010049,0.0008427544,0.002601549,0.00002360642,0.001033643,0.00008604252,0.00009758989,0.0004103843],"genre_scores_gemma":[0.9912904,0.00007037714,0.005065725,0.003385696,0.00001612056,0.00009122929,0.00006363602,0.00001161479,0.000005217581],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6644041,"threshold_uncertainty_score":0.5302154,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03397674542914188,"score_gpt":0.341702568126696,"score_spread":0.3077258226975542,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}