{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0009218839,0.0005009745,0.0006249042,0.0001597966,0.0004618276,0.000162627,0.0008250709,0.0004743701,0.00001877486],"category_scores_gemma":[0.0006412391,0.0005185097,0.0003231659,0.0001454992,0.0001265109,0.00005010655,0.0003752464,0.0001961922,0.00001060372],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004735596,"about_ca_system_score_gemma":0.000170439,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002011697,"about_ca_topic_score_gemma":0.0001735171,"domain_scores_codex":[0.997242,0.0002043952,0.0006918389,0.0008427759,0.0005104317,0.0005085372],"domain_scores_gemma":[0.9971856,0.00004727783,0.0004831861,0.001690962,0.0003376943,0.0002552665],"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":[0.00006165793,0.00005879142,0.000008602242,0.000140251,0.0003306533,0.00003095865,0.0001380631,0.00003509135,0.9086192,0.08922353,0.00001658866,0.001336563],"study_design_scores_gemma":[0.0005303112,0.0003544778,0.000004938724,0.0001308444,0.0005249273,0.00003901653,0.0003151947,0.004006719,0.9533746,0.04014635,0.00006047714,0.0005120983],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7458217,0.0009413318,0.2515565,0.0005297213,0.000238174,0.0005904607,0.0001891193,0.00003375674,0.00009921296],"genre_scores_gemma":[0.9963927,0.000473713,0.001842965,0.0004387684,0.00008315678,0.0001148416,0.0005215555,0.0001038421,0.00002849919],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.250571,"threshold_uncertainty_score":0.9997267,"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."}}