{"id":"W2701364055","doi":"10.1021/acscatal.7b01554","title":"Enzymatic Post-Transfer Editing Mechanism of <i>E. coli</i> Threonyl-tRNA Synthetase (ThrRS): A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Investigation","year":2017,"lang":"en","type":"article","venue":"ACS Catalysis","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Windsor","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Aminoacylation; Molecular mechanics; Chemistry; QM/MM; Active site; Molecular dynamics; Protonation; Deprotonation; Stereochemistry; Transfer RNA; Enzyme; Biochemistry; Computational chemistry; RNA; Organic chemistry","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001295963,0.000315344,0.0002568763,0.00008679595,0.0003045204,0.0002373765,0.0003932186,0.0003316114,0.0006918467],"category_scores_gemma":[0.0002012297,0.000157837,0.0003235037,0.00009142606,0.0003064297,0.0003795137,0.0001888164,0.0003118246,0.00008890696],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003792307,"about_ca_system_score_gemma":0.0004816361,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002839511,"about_ca_topic_score_gemma":0.001645942,"domain_scores_codex":[0.9999517,0.00001046019,0.000002392396,0.00001111949,0.0000117086,0.00001267563],"domain_scores_gemma":[0.999943,0.00001504384,0.00001476613,0.000006325404,0.0000105558,0.0000102149],"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":[0.0003987367,0.0003166902,0.009784929,0.0003917186,0.0001514096,0.0007523247,0.0002270889,0.6078314,0.3370039,0.0220774,0.0004823205,0.02058211],"study_design_scores_gemma":[0.00004451346,0.0001951989,0.002715123,0.000008614764,0.00003001846,0.0001071361,0.00005622168,0.9539075,0.04028942,0.001598267,0.001012046,0.00003600865],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9819004,0.0003920296,0.0149215,0.0001752494,0.00002167713,0.00002154699,0.00005872002,0.0000536944,0.002455197],"genre_scores_gemma":[0.9936651,0.0003353275,0.005478458,0.00001760317,0.000004770328,0.00001715533,0.00006668492,0.000009607221,0.0004053435],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002839511,"threshold_uncertainty_score":0.005645931,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00799272888012666,"score_gpt":0.2180697253950092,"score_spread":0.2100769965148825,"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."}}