{"id":"W4406310309","doi":"10.1021/acs.jproteome.4c00618","title":"Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor","year":2025,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Ubiquitin and proteasome pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"Discovery Centre","funders":"Chinese Academy of Medical Sciences; Alzheimer’s Research UK; University of Oxford","keywords":"Ubiquitin; Covalent bond; Chemistry; Biochemistry; Protease; Computational biology; Enzyme; Biology; Organic chemistry","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00206589,0.0001495331,0.0002875499,0.00030207,0.0001296776,0.00004601646,0.0005723695,0.0001256052,0.00003735936],"category_scores_gemma":[0.0003152083,0.00009555838,0.0001241576,0.0005824128,0.0002989091,0.00001114121,0.0002990243,0.0007310683,0.000001002649],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001455115,"about_ca_system_score_gemma":0.0007276465,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003041404,"about_ca_topic_score_gemma":0.00008516249,"domain_scores_codex":[0.9976659,0.0005190863,0.0005581511,0.0002185546,0.0006402323,0.0003980741],"domain_scores_gemma":[0.9985151,0.00004729306,0.0002866325,0.0003521702,0.0007098787,0.00008894042],"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":[0.00257308,0.0001143901,0.02054502,0.0002788799,0.00007082237,0.00003818086,0.000201766,0.0001301919,0.972732,0.0009083223,0.0003630356,0.002044324],"study_design_scores_gemma":[0.003035535,0.002224215,0.02621553,0.000810964,0.00001186854,0.0001430799,0.0008978864,0.0006185115,0.9616222,0.001253801,0.002972085,0.0001942851],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9959722,0.0004146991,0.0002802112,0.00121195,0.00006672604,0.001208522,0.00002269693,0.00000218801,0.000820787],"genre_scores_gemma":[0.9979035,0.00004564145,0.001446569,0.00003357754,0.0001906071,0.00005107289,0.000007796994,0.00001697013,0.000304232],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01110974,"threshold_uncertainty_score":0.3896758,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05184947735217938,"score_gpt":0.3377407304680636,"score_spread":0.2858912531158842,"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."}}