{"id":"W2014827569","doi":"10.1021/jp807104b","title":"Substrate-assisted Catalysis in the Aminoacyl Transfer Mechanism of Histidyl−tRNA Synthetase: A Density Functional Theory Study","year":2008,"lang":"en","type":"article","venue":"The Journal of Physical Chemistry B","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Windsor","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Aminoacylation; Chemistry; Moiety; Concerted reaction; Stereochemistry; Transfer RNA; Density functional theory; Transition state; Ribose; Oxygen; Catalysis; Enzyme; Computational chemistry; RNA; Biochemistry; 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":[],"consensus_categories":[],"category_scores_codex":[0.0006708942,0.0001985334,0.0003193423,0.00001595611,0.0001125936,0.000007596957,0.0005681507,0.00009323602,0.00003271698],"category_scores_gemma":[0.00009422409,0.000117351,0.0002839948,0.0001499198,0.0002738117,0.000007914186,0.00005254241,0.000360838,0.000001530003],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002463926,"about_ca_system_score_gemma":0.000109936,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000118286,"about_ca_topic_score_gemma":0.000004147565,"domain_scores_codex":[0.9986235,0.0001725898,0.0004069363,0.0001705607,0.0004386333,0.0001878174],"domain_scores_gemma":[0.9990051,0.0001310459,0.0001957095,0.0004453617,0.0001563518,0.00006646752],"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":[0.0005825746,0.001209648,0.0004204018,0.00002747204,0.0002062822,0.00004504934,0.0006987108,0.00005538576,0.9964766,0.00003183267,0.0001483328,0.00009774154],"study_design_scores_gemma":[0.000839484,0.0002173405,0.007327573,0.00001602107,0.0002543974,0.0004978584,0.001541397,0.00002453486,0.9888246,0.0002696763,0.00005047522,0.0001366114],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9987571,0.0001361148,0.0004208225,0.00006890464,0.00002530103,0.00008564792,0.00001083734,0.000002974914,0.0004923246],"genre_scores_gemma":[0.9994286,0.00003123118,0.000009158009,0.00004174886,0.0002944331,0.000004125519,0.00001762855,0.00001460874,0.0001584307],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007651938,"threshold_uncertainty_score":0.4785436,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01400365826673643,"score_gpt":0.2205231759600458,"score_spread":0.2065195176933094,"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."}}