{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003443335,0.0003769464,0.0004183962,0.0002241529,0.0005711855,0.0005079134,0.0008892925,0.0005250453,0.002567889],"category_scores_gemma":[0.000572228,0.0003126188,0.0004641535,0.0001681372,0.0008137194,0.0006620422,0.0006294969,0.0008268055,0.000355452],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006001141,"about_ca_system_score_gemma":0.0006823246,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003229594,"about_ca_topic_score_gemma":0.001023124,"domain_scores_codex":[0.9998327,0.00002799054,0.000009822924,0.00003063372,0.00005789523,0.00004090903],"domain_scores_gemma":[0.9998848,0.00003159543,0.00001667295,0.00002127217,0.0000241129,0.00002156833],"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":[0.0004410299,0.0002111983,0.006053665,0.001005684,0.0001684207,0.0009633961,0.0004177708,0.5031725,0.2495747,0.2063375,0.002807281,0.02884695],"study_design_scores_gemma":[0.00004847639,0.0001632777,0.002037172,0.00003263347,0.00002525165,0.000134907,0.0001119938,0.9476494,0.02989818,0.01647987,0.003370324,0.00004857098],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8300737,0.003550795,0.1298207,0.001845839,0.0002484917,0.0001298114,0.0004090806,0.0003945746,0.03352702],"genre_scores_gemma":[0.990496,0.0007922626,0.007515846,0.00007923309,0.00001607912,0.00007301898,0.0001117782,0.00003625611,0.0008795591],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003229594,"threshold_uncertainty_score":0.00859046,"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."}}