{"id":"W4414900204","doi":"10.1261/rna.080619.125","title":"<i>ykkC</i> -I riboswitch aptamer domain requires an interplay between metal triad and cationic ligand: insights into metal ion–induced allostery from molecular dynamics simulations","year":2025,"lang":"en","type":"article","venue":"RNA","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge","funders":"","keywords":"Riboswitch; Aptamer; Isothermal titration calorimetry; Allosteric regulation; RNA; RNase P; RNase H; Molecular dynamics; Ligand (biochemistry)","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":[0.0001448287,0.0002998941,0.0003894702,0.0001412894,0.00053514,0.0005637729,0.0004929469,0.000595442,0.003160428],"category_scores_gemma":[0.0002754122,0.0002135067,0.0003374114,0.0001175886,0.0005022276,0.0005172236,0.0002536456,0.0005198159,0.0002149457],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001010385,"about_ca_system_score_gemma":0.0008704728,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008304264,"about_ca_topic_score_gemma":0.006386212,"domain_scores_codex":[0.999938,0.000008110336,0.000001969902,0.00001168947,0.00001208824,0.0000281008],"domain_scores_gemma":[0.9999169,0.00002849836,0.00001534629,0.000004364516,0.00001039758,0.00002447977],"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":[0.0004070907,0.0002739536,0.003765433,0.0001263382,0.00008302625,0.0007119355,0.0001747131,0.8823178,0.09152073,0.01528126,0.001325465,0.004012298],"study_design_scores_gemma":[0.00007508228,0.00007892928,0.001055307,0.000007342016,0.0000120843,0.00002445605,0.00004227481,0.9899839,0.007147457,0.001090078,0.0004674143,0.0000156434],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9906274,0.00005133218,0.004163998,0.0001572622,0.00002100135,0.00001865154,0.0001009113,0.00008040511,0.004779032],"genre_scores_gemma":[0.9974365,0.00005763103,0.001584403,0.00005499333,0.000003545386,0.00003704878,0.0001218368,0.00003437508,0.0006696502],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008304264,"threshold_uncertainty_score":0.01651186,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01047833739543182,"score_gpt":0.2834911966720234,"score_spread":0.2730128592765916,"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."}}