{"id":"W4412068146","doi":"10.3390/pr13072151","title":"Effects of Denaturants on Early-Stage Prion Conversion: Insights from Molecular Dynamics Simulations","year":2025,"lang":"en","type":"article","venue":"Processes","topic":"Prion Diseases and Protein Misfolding","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Alberta Innovates","keywords":"Stage (stratigraphy); Dynamics (music); Molecular dynamics; Prion protein; Statistical physics; Computational biology; Chemistry; Biological system; Biology; Physics; Medicine; Computational chemistry; Internal medicine","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00001470721,0.0001073628,0.000107506,0.00005047968,0.00005961122,0.00001635933,0.0001445043,0.0001040735,0.00000834922],"category_scores_gemma":[0.0002680536,0.0001002393,0.00004729932,0.0001576574,0.00003211781,0.000005157938,0.0000725581,0.0000543852,0.000002604956],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001533853,"about_ca_system_score_gemma":0.0001434159,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002854463,"about_ca_topic_score_gemma":0.00001453164,"domain_scores_codex":[0.9994226,0.00002848616,0.0001219674,0.0002305876,0.000100627,0.00009569353],"domain_scores_gemma":[0.9995361,0.00006345254,0.00006761134,0.0001753744,0.0001191164,0.00003833166],"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":[0.0005484901,0.0003070683,0.008387873,0.002957716,0.0002618858,0.00002027198,0.0001326103,0.001883551,0.9726382,0.00090428,0.0000904968,0.01186756],"study_design_scores_gemma":[0.0005561009,0.00009174087,0.003045017,0.0001856942,0.00004163443,9.18205e-8,0.00001599855,0.0006370243,0.9916692,0.0008092968,0.002829314,0.0001188861],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9746781,0.02028399,0.004456052,0.0000468752,0.00008401914,0.0002250269,0.00003970821,0.0000126654,0.0001735852],"genre_scores_gemma":[0.9982663,0.001065978,0.0001784491,0.0001997509,0.00002254382,0.00001092099,0.000124585,0.000009248839,0.0001222263],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02358822,"threshold_uncertainty_score":0.408764,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00315117719647836,"score_gpt":0.2358491530249927,"score_spread":0.2326979758285144,"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."}}