{"id":"W4406938434","doi":"10.1101/2025.01.28.635154","title":"Customizing the Structure of Minimal TIM Barrels to Craft Efficient <i>De Novo</i> Enzymes","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Peptidase Inhibition and Analysis","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"","keywords":"Barrel (horology); Active site; Enzyme; Chemistry; Catalysis; Substrate (aquarium); Protein engineering; Stereochemistry; Nanotechnology; Biochemistry; Computational biology; Biology; Materials science","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":[0.0004313773,0.0004179026,0.000346265,0.000129927,0.0001212906,0.0004846776,0.0004597705,0.0002679979,0.0009796278],"category_scores_gemma":[0.0004289107,0.0002142889,0.0003296844,0.0001150167,0.0001792986,0.0002777718,0.0004505393,0.0005303728,0.0003690703],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003329323,"about_ca_system_score_gemma":0.000305986,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002447111,"about_ca_topic_score_gemma":0.0003547244,"domain_scores_codex":[0.9998881,0.00002168536,0.000009264731,0.00002878581,0.00002856578,0.00002354205],"domain_scores_gemma":[0.9998763,0.00002861471,0.00003120485,0.00002138109,0.00002171361,0.00002075686],"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":[0.0004962203,0.0001669234,0.002001017,0.0002352258,0.00006928801,0.0001389959,0.00005924545,0.1121553,0.8566674,0.003479782,0.0004454428,0.02408522],"study_design_scores_gemma":[0.00005400456,0.000608677,0.0007774676,0.00001498169,0.00005062688,0.0001114622,0.000033155,0.2401558,0.7505475,0.0007295373,0.006886484,0.00003019471],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8550521,0.0005197617,0.1404175,0.0000886629,0.00004892714,0.00007232059,0.0003288563,0.001066706,0.002405209],"genre_scores_gemma":[0.9217438,0.0002741338,0.07655523,0.00003455557,0.00000524905,0.00006111906,0.0003467899,0.0001627849,0.0008163377],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009796278,"threshold_uncertainty_score":0.003277183,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008827361337141727,"score_gpt":0.2387911972905272,"score_spread":0.2299638359533855,"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."}}