{"id":"W2596491515","doi":"10.1016/j.chembiol.2017.02.013","title":"Polyubiquitin-Photoactivatable Crosslinking Reagents for Mapping Ubiquitin Interactome Identify Rpn1 as a Proteasome Ubiquitin-Associating Subunit","year":2017,"lang":"en","type":"article","venue":"Cell chemical biology","topic":"Ubiquitin and proteasome pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":45,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto","funders":"National Institute of Neurological Disorders and Stroke; National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Seventh Framework Programme; National Institutes of Health; Technion-Israel Institute of Technology; Israel Science Foundation","keywords":"Ubiquitin; Interactome; Proteasome; Deubiquitinating enzyme; Protein subunit; Chemistry; Docking (animal); Biochemistry; Computational biology; Cell biology; Biology; 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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000912348,0.0005456668,0.0006192249,0.0001057489,0.0009630934,0.0003683899,0.00134528,0.0008414774,0.0001542142],"category_scores_gemma":[0.001989183,0.0005659431,0.0004026656,0.00008753138,0.0003771317,0.00003955487,0.001101433,0.0005227048,0.00009205958],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001070972,"about_ca_system_score_gemma":0.0001965683,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001453196,"about_ca_topic_score_gemma":0.00001131526,"domain_scores_codex":[0.9964061,0.0001542411,0.0007501849,0.001205122,0.0001979798,0.001286417],"domain_scores_gemma":[0.9971094,0.000176238,0.0009521896,0.001156746,0.000302013,0.0003034156],"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":[0.0002463293,0.0001621778,0.003242328,0.0001809946,0.00009893343,0.000008320643,0.0002000113,2.950876e-7,0.9931638,0.0003078048,0.0005041103,0.001884871],"study_design_scores_gemma":[0.001670878,0.0003460292,0.0004003212,0.0001291524,0.00003495602,0.00003494869,0.0001452473,0.00003397007,0.9527359,0.002189002,0.04162255,0.000657052],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9842866,0.0003470127,0.0009586749,0.0003694292,0.0004783118,0.001278976,0.0002680342,0.00008636944,0.01192659],"genre_scores_gemma":[0.9917634,0.00005415695,0.002469664,0.0007340859,0.001324527,0.0005505462,0.0009048206,0.0001100677,0.002088808],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04111844,"threshold_uncertainty_score":0.9996792,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03309276739646436,"score_gpt":0.320133986583577,"score_spread":0.2870412191871126,"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."}}