{"id":"W1567757436","doi":"10.1002/pmic.201500058","title":"The use of ubiquitin lysine mutants to characterize E2–E3 linkage specificity: Mass spectrometry offers a cautionary “tail”","year":2015,"lang":"en","type":"article","venue":"PROTEOMICS","topic":"Ubiquitin and proteasome pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University of Toronto; University Health Network","funders":"Canadian Institutes of Health Research","keywords":"Ubiquitin; Lysine; Mutant; Linkage (software); Ubiquitin-conjugating enzyme; Computational biology; Biology; Biochemistry; Chemistry; Ubiquitin ligase; Genetics; Amino acid; Gene","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":[0.001325677,0.0007005869,0.0004398972,0.0004412368,0.000460656,0.0007028044,0.0004529743,0.0008318218,0.000891562],"category_scores_gemma":[0.0008728241,0.0002949647,0.0004384061,0.0003834444,0.0006367544,0.0005500608,0.0004676649,0.0009655792,0.0005440383],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002570233,"about_ca_system_score_gemma":0.000192472,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004376426,"about_ca_topic_score_gemma":0.001099526,"domain_scores_codex":[0.9989336,0.0003160159,0.000177822,0.0002348894,0.0002453144,0.00009238272],"domain_scores_gemma":[0.9990302,0.0004141785,0.0001640536,0.0002245189,0.0001147905,0.00005212999],"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":[0.00006063234,0.00002182259,0.0006360754,0.00004115843,0.00001982256,0.00003403392,0.00001905999,0.00005267844,0.9975006,0.00008886075,0.00004731211,0.001477964],"study_design_scores_gemma":[0.000002329361,0.0000542936,0.001528942,0.000001811938,0.00001012899,0.000236543,0.000009505673,0.0002177839,0.9970783,0.00005922469,0.0007960522,0.000004989438],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8694785,0.002736192,0.1231447,0.0005374259,0.0001188495,0.0001558705,0.0006366058,0.0004510542,0.002740766],"genre_scores_gemma":[0.8957462,0.001459164,0.09808917,0.0006230828,0.00002163109,0.0001356581,0.0007085775,0.0001917842,0.003024664],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001325677,"threshold_uncertainty_score":0.007010937,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06431325323818271,"score_gpt":0.256978383144932,"score_spread":0.1926651299067493,"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."}}