{"id":"W4398167156","doi":"10.26508/lsa.202402740","title":"K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors","year":2024,"lang":"en","type":"article","venue":"Life Science Alliance","topic":"Ubiquitin and proteasome pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Genentech; Ontario Genomics Institute; European Federation of Pharmaceutical Industries and Associations; Structural Genomics Consortium; Merck KGaA; Ontario Genomics; Genome Canada; Innovative Medicines Canada; Bayer; European Commission; Pfizer; Deutsche Forschungsgemeinschaft; Bristol-Myers Squibb","keywords":"Ubiquitin; Interactome; Cell biology; Deubiquitinating enzyme; Chain (unit); Computational biology; Biology; Chemistry; Genetics; Physics; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0009204995,0.0002811599,0.0002361518,0.0001106622,0.0002194065,0.0004364718,0.0004425652,0.0001333587,0.00007511801],"category_scores_gemma":[0.0003081906,0.0002543678,0.00006403092,0.0003661365,0.0007751642,0.00006806446,0.0003669386,0.0002747064,0.00005671105],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002755285,"about_ca_system_score_gemma":0.0001481307,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008518497,"about_ca_topic_score_gemma":0.000009003921,"domain_scores_codex":[0.9977131,0.00007436937,0.000350522,0.001013458,0.0002924427,0.0005560823],"domain_scores_gemma":[0.9990023,0.00007557679,0.00008643646,0.0004054219,0.00008805276,0.0003421861],"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":[0.00004490619,0.00002200691,0.001147125,0.0001178526,0.00001728477,0.00001390253,0.0006118241,0.000001723248,0.9767678,0.002436795,0.001324489,0.01749428],"study_design_scores_gemma":[0.000624406,0.0005806818,0.0127852,0.0007282381,0.00001756708,0.0001558405,0.0004999762,0.0007252177,0.6371285,0.001588662,0.3441855,0.0009801983],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9859848,0.009293579,0.0005101074,0.001274791,0.0006739751,0.0003666465,0.00004555495,0.00006808279,0.001782438],"genre_scores_gemma":[0.9938605,0.002261815,0.0007474733,0.001135407,0.0005424932,0.00005101215,0.00001955206,0.0000321788,0.00134954],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.342861,"threshold_uncertainty_score":0.9999909,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01992198211761613,"score_gpt":0.2795098406112352,"score_spread":0.259587858493619,"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."}}