{"id":"W1961260837","doi":"10.1002/prot.24732","title":"Multiple proton relay routes in the reaction mechanism of <scp>RNAP</scp> II: Assessing the effect of structural model","year":2014,"lang":"en","type":"article","venue":"Proteins Structure Function and Bioinformatics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"","keywords":"Pyrophosphate; Chemistry; Proton; Active site; Molecular dynamics; Protein Data Bank (RCSB PDB); Yield (engineering); Reaction mechanism; Substrate (aquarium); Density functional theory; Catalysis; Stereochemistry; Enzyme; Computational chemistry; Physics; Biochemistry; Thermodynamics","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007176851,0.0001980423,0.0002137282,0.0000625078,0.0002090819,0.00004120679,0.0001883626,0.0002154261,0.000002013551],"category_scores_gemma":[0.0004511361,0.0001025299,0.00007779164,0.0001220951,0.00007891256,0.00003414924,0.0000784459,0.0001751382,2.219799e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008348292,"about_ca_system_score_gemma":0.00002517831,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000195718,"about_ca_topic_score_gemma":0.00001418872,"domain_scores_codex":[0.9988498,0.0001784738,0.0003995365,0.0001486873,0.0002475084,0.0001759626],"domain_scores_gemma":[0.9990779,0.00009761449,0.0003953592,0.000335051,0.00006493994,0.00002909138],"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":[0.00006732193,0.000008476752,0.00111817,0.000281799,0.00003083701,5.4637e-8,0.0005633191,0.0004704683,0.9847638,0.0008757802,0.000017249,0.01180274],"study_design_scores_gemma":[0.000704593,0.001124012,0.001241106,0.00005363519,0.00004451552,0.000017712,0.0003959024,0.0650285,0.928302,0.00267155,0.0003397366,0.00007674689],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9497311,0.00007254681,0.04833044,0.00004553299,0.0001141701,0.001426231,0.00001532288,0.000009613637,0.0002550868],"genre_scores_gemma":[0.9949581,0.0000152604,0.004711734,0.00007213287,0.00007112,0.00008324636,0.00004162698,0.00001186656,0.0000348966],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06455804,"threshold_uncertainty_score":0.4181047,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006462048905190229,"score_gpt":0.2215247024618003,"score_spread":0.2150626535566101,"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."}}