{"id":"W4406852069","doi":"10.1101/2025.01.26.634918","title":"Distal mutations in a designed retro-aldolase alter loop dynamics to shift and accelerate the rate-limiting step","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Photosynthetic Processes and Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada; Ministerio de Ciencia e Innovación; Alliance de recherche numérique du Canada; Generalitat de Catalunya","keywords":"Limiting; Aldolase A; Dynamics (music); Loop (graph theory); Control theory (sociology); Computer science; Chemistry; Physics; Mathematics; Engineering; Biochemistry; Artificial intelligence; Enzyme; Control (management); Mechanical engineering","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":[0.0001480086,0.0003178725,0.0001912027,0.0001062595,0.0001077451,0.0003119254,0.0002961076,0.0002097037,0.001236395],"category_scores_gemma":[0.0001970589,0.0001058465,0.0001843378,0.0001232567,0.0002800254,0.0001657199,0.0002408467,0.000540934,0.0002295229],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003020312,"about_ca_system_score_gemma":0.0002065603,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007234783,"about_ca_topic_score_gemma":0.0009329617,"domain_scores_codex":[0.9999141,0.00001319599,0.000007701798,0.00001745797,0.00003221394,0.00001538726],"domain_scores_gemma":[0.9999224,0.00002195796,0.00002094372,0.000009795243,0.000007280436,0.00001761742],"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":[0.0002961837,0.00009317949,0.0008747182,0.00003633321,0.00002481086,0.0001359716,0.00002125074,0.004361801,0.9907544,0.0006923852,0.00005430536,0.002654675],"study_design_scores_gemma":[0.00004602819,0.0002122867,0.001302059,0.000006405039,0.00002215458,0.0001796375,0.00002880022,0.02083514,0.9759403,0.0001866867,0.001226295,0.00001418768],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955648,0.00008853046,0.003693722,0.00003167709,0.00001246159,0.0000100224,0.00006881608,0.00006768912,0.000462298],"genre_scores_gemma":[0.9972219,0.00004721781,0.002263796,0.00001331005,0.000001355156,0.000004067724,0.00005359115,0.00002122718,0.0003734936],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001236395,"threshold_uncertainty_score":0.004136205,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009747050860842588,"score_gpt":0.2306148913120781,"score_spread":0.2208678404512355,"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."}}