{"id":"W2411345956","doi":"10.1016/bs.mie.2014.10.055","title":"Using Reweighted Pulling Simulations to Characterize Conformational Changes in Riboswitches","year":2015,"lang":"en","type":"article","venue":"Methods in enzymology on CD-ROM/Methods in enzymology","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"European Commission; Université de Sherbrooke","keywords":"Riboswitch; Aptamer; Stacking; Molecular dynamics; Ligand (biochemistry); Computational biology; Biophysics; Chemistry; RNA; Biological system; Biology; Gene; Computational chemistry; Genetics; Biochemistry; Non-coding RNA","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004130797,0.0007642464,0.0005659763,0.0002652637,0.0006941407,0.0004504762,0.0007793765,0.0007272298,0.002493655],"category_scores_gemma":[0.001094006,0.0004508839,0.0004656852,0.0003390077,0.0004458161,0.0009511735,0.0004184182,0.001177623,0.0002227797],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008365648,"about_ca_system_score_gemma":0.0007333272,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003848027,"about_ca_topic_score_gemma":0.005636393,"domain_scores_codex":[0.9998865,0.00002178618,0.000005142751,0.00002730116,0.00002965501,0.0000296116],"domain_scores_gemma":[0.9995735,0.0002394646,0.00003928709,0.00005517284,0.00004690011,0.00004558791],"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":[0.0003196231,0.0003039568,0.00200286,0.000139473,0.0001502454,0.0002769689,0.0001939938,0.9198047,0.06030176,0.006906796,0.0007527862,0.008846784],"study_design_scores_gemma":[0.00003410559,0.00007796712,0.0003491579,0.000004321194,0.00001256547,0.000008620414,0.00002480082,0.9921664,0.00619863,0.000911578,0.0001979495,0.00001399692],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9842104,0.00009122417,0.01246458,0.0001273808,0.00003822807,0.00004430112,0.0001351339,0.0002030619,0.002685623],"genre_scores_gemma":[0.9894225,0.00009939448,0.009079631,0.00008081254,0.00001112936,0.0001049635,0.0002495962,0.0001352526,0.0008168361],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003848027,"threshold_uncertainty_score":0.008342087,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1473371944347648,"score_gpt":0.4302125562120424,"score_spread":0.2828753617772777,"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."}}