{"id":"W4317433395","doi":"10.1021/acs.biochem.2c00479","title":"Mutation Effects on Structure and Dynamics: Adaptive Evolution of the SARS-CoV-2 Main Protease","year":2023,"lang":"en","type":"article","venue":"Biochemistry","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Eye Institute; Division of Graduate Education; University of California, Irvine; Nuclear Safety and Security Commission; Canadian Institute for Advanced Research; National Aeronautics and Space Administration; Division of Mathematical Sciences; National Institutes of Health; National Science Foundation","keywords":"Protease; Active site; Protein tertiary structure; Mutation; Biology; Protein structure; Phylogenetic tree; Computational biology; Genetics; Evolutionary dynamics; Viral replication; Silent mutation; Protein secondary structure; Virus; Enzyme; Gene; Biochemistry; Missense mutation; Medicine","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002275932,0.0002936221,0.0001990903,0.0002771452,0.0002431665,0.0003177553,0.0002322998,0.000318887,0.0008609228],"category_scores_gemma":[0.001187403,0.000103228,0.0002643288,0.0002354703,0.000386944,0.0003515706,0.0002359983,0.0003023795,0.00007347255],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004525464,"about_ca_system_score_gemma":0.0002905168,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00290774,"about_ca_topic_score_gemma":0.002774614,"domain_scores_codex":[0.9999058,0.00003500492,0.000006059308,0.00001608601,0.00001975853,0.00001724978],"domain_scores_gemma":[0.9998019,0.00009161634,0.00004538054,0.00001126139,0.00001904886,0.00003073051],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00106481,0.0005152597,0.08921077,0.00016978,0.0003120509,0.001148891,0.0003505971,0.5946375,0.289819,0.006020687,0.0004695088,0.01628126],"study_design_scores_gemma":[0.00009048333,0.0006219827,0.08566903,0.00001531517,0.00009428493,0.0003601556,0.0002474619,0.8874669,0.02273633,0.002049989,0.0006019834,0.00004601281],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9992008,0.00004313888,0.0004244137,0.00002624981,0.000001747438,0.000002405221,0.00002775659,0.000008303748,0.0002653061],"genre_scores_gemma":[0.9994007,0.00005234964,0.0004427386,0.000007849268,0.000001212202,0.000003389674,0.00003761519,0.000004509953,0.00004953614],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00290774,"threshold_uncertainty_score":0.005781651,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01566823748691578,"score_gpt":0.3029194866334081,"score_spread":0.2872512491464924,"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."}}