{"id":"W1096325687","doi":"10.1371/journal.pone.0134879","title":"Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization","year":2015,"lang":"en","type":"article","venue":"PLoS ONE","topic":"RNA modifications and cancer","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Canadian Institutes of Health Research; National Natural Science Foundation of China","keywords":"Allosteric regulation; Dimer; Chemistry; Molecular dynamics; Binding site; Stereochemistry; Catalytic cycle; Molecule; Catalysis; Biophysics; Computational chemistry; Enzyme; Biochemistry; Biology","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000429408,0.000873806,0.001170814,0.0005825765,0.001903291,0.0007104076,0.001391311,0.001324295,0.003524788],"category_scores_gemma":[0.001109351,0.0005350607,0.001073941,0.0006903418,0.0008499475,0.0009252729,0.0006329969,0.001380712,0.0002323029],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001555177,"about_ca_system_score_gemma":0.001599348,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02186246,"about_ca_topic_score_gemma":0.01550386,"domain_scores_codex":[0.999798,0.00003942049,0.000008349405,0.00003457463,0.00003565276,0.00008402561],"domain_scores_gemma":[0.9993247,0.0003259797,0.00004862248,0.00003337723,0.0001284271,0.0001389723],"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":[0.0004922127,0.000546465,0.00725318,0.0001954259,0.0002188142,0.000623163,0.0003837362,0.9644189,0.00891054,0.01163372,0.001864017,0.003459803],"study_design_scores_gemma":[0.00009600281,0.0001007116,0.001360144,0.00001393023,0.00002724103,0.00001584987,0.00009003685,0.9960406,0.0007593984,0.001021958,0.00045735,0.00001674677],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9846739,0.0004872496,0.004867831,0.0006178186,0.00006551345,0.0000541919,0.0006218215,0.0001251519,0.008486573],"genre_scores_gemma":[0.991763,0.0004108677,0.005261319,0.0001359287,0.00002572215,0.0001713871,0.001015124,0.0000532318,0.001163327],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02186246,"threshold_uncertainty_score":0.04347038,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04854227717740043,"score_gpt":0.2797511223960332,"score_spread":0.2312088452186328,"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."}}