{"id":"W4280553819","doi":"10.2196/37391","title":"In Silico Comparative Analysis of the Functional, Structural, and Evolutionary Properties of SARS-CoV-2 Variant Spike Proteins","year":2022,"lang":"en","type":"article","venue":"JMIR Bioinformatics and Biotechnology","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Spike (software development); Biology; In silico; Phylogenetic tree; Computational biology; Genetics; Sequence analysis; UniProt; Isoelectric point; Antigenicity; Coronavirus; Gene; Coronavirus disease 2019 (COVID-19); Biochemistry; Computer science; Enzyme","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":[0.0001247858,0.000121768,0.0002724308,0.0002424647,0.000127208,0.000008288635,0.0001815272,0.0001242805,0.000004658781],"category_scores_gemma":[0.000015732,0.00008189436,0.00007175368,0.0005323271,0.0002515961,0.00001432521,0.0005612059,0.0001489619,1.262439e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001300565,"about_ca_system_score_gemma":0.00004898247,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006352273,"about_ca_topic_score_gemma":0.0000425927,"domain_scores_codex":[0.9991664,0.00002715097,0.0004431742,0.0001142056,0.0001177681,0.0001312811],"domain_scores_gemma":[0.9993871,0.000005067412,0.000278013,0.0002745316,0.00004477727,0.00001052384],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002153391,0.0001360893,0.004558669,0.0002565838,0.0006497903,4.268317e-7,0.001588571,0.0008440106,0.9851404,0.005262713,0.0005609993,0.0007864124],"study_design_scores_gemma":[0.001509175,0.001166725,0.06437739,0.0000383954,0.0002499222,0.0001493543,0.008074509,0.1269925,0.789371,0.0004244724,0.007201826,0.0004447087],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9980969,0.0007097889,0.0001026059,0.0004736851,0.00003534013,0.0004377134,0.00006926954,0.000004680835,0.00007003722],"genre_scores_gemma":[0.9989482,0.000100093,0.000726696,0.0001017659,0.000005070771,0.00005928535,0.00003626537,0.000003385385,0.00001929724],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1957694,"threshold_uncertainty_score":0.3339555,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02620009133363341,"score_gpt":0.2464685330408121,"score_spread":0.2202684417071787,"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."}}