{"id":"W4301595053","doi":"10.1002/prot.26433","title":"Fundamentals behind the specificity of <scp>Cysteinyl‐tRNA</scp> synthetase: <scp>MD</scp> and <scp>QM</scp> / <scp>MM</scp> joint investigations","year":2022,"lang":"en","type":"article","venue":"Proteins Structure Function and Bioinformatics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Windsor","funders":"China Scholarship Council; National Natural Science Foundation of China","keywords":"Aminoacylation; Chemistry; Cysteine; QM/MM; Molecular mechanics; Amino acid; Transfer RNA; Serine; Substrate (aquarium); Molecular dynamics; Stereochemistry; Enzyme; Biochemistry; Computational chemistry; RNA; Biology","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":["metaepi_narrow","sts"],"consensus_categories":[],"category_scores_codex":[0.001103016,0.0007868144,0.0007210107,0.0003128762,0.001534178,0.0003487041,0.00058566,0.0005041793,0.00005709333],"category_scores_gemma":[0.001870754,0.0006247111,0.0003023291,0.0004778122,0.0006148029,0.0001055491,0.0008093972,0.000744595,0.00001686632],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008553464,"about_ca_system_score_gemma":0.0002431215,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005565547,"about_ca_topic_score_gemma":0.00006140867,"domain_scores_codex":[0.9957571,0.0004052366,0.001301091,0.00072398,0.0009635219,0.0008490664],"domain_scores_gemma":[0.9965867,0.0004689056,0.001236956,0.001014951,0.000258876,0.0004336585],"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":[0.00002205154,0.0002345144,0.002039309,0.0009504095,0.0006953321,0.00000815279,0.005414868,0.0004133953,0.9450979,0.003002763,0.03481159,0.007309763],"study_design_scores_gemma":[0.00130396,0.00139318,0.001965084,0.0001028217,0.000295952,0.0002866245,0.01523189,0.0009790383,0.662613,0.004374596,0.311319,0.0001348192],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9782015,0.003496057,0.009105901,0.0001731134,0.001046636,0.002853235,0.001345407,0.0001117554,0.003666365],"genre_scores_gemma":[0.9775875,0.00103423,0.01186862,0.001421704,0.0007029201,0.0005150158,0.001068335,0.0001430085,0.005658643],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2824848,"threshold_uncertainty_score":0.9997657,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01421748485495468,"score_gpt":0.2080339130683282,"score_spread":0.1938164282133736,"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."}}