{"id":"W4403428249","doi":"10.1038/s41467-024-52871-9","title":"Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders","year":2024,"lang":"en","type":"article","venue":"Nature Communications","topic":"Protein Degradation and Inhibitors","field":"Biochemistry, Genetics and Molecular Biology","cited_by":38,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Japan Society for the Promotion of Science; European Commission; Eisai; European Federation of Pharmaceutical Industries and Associations; McGill University; Diamond Light Source; University of Dundee","keywords":"Cereblon; Computational biology; Ubiquitin ligase; Signal transducing adaptor protein; Computer science; Chemistry; Cell biology; Ubiquitin; Biology; Biochemistry; Signal transduction","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":[],"consensus_categories":[],"category_scores_codex":[0.0001275037,0.00006998207,0.0001101829,0.00006481404,0.00005336266,0.000007244583,0.0001961218,0.0001352489,6.091495e-7],"category_scores_gemma":[0.000170351,0.00005987474,0.00005792295,0.000141622,0.0004294982,0.000004023879,0.0001038289,0.0001275813,8.21517e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003619875,"about_ca_system_score_gemma":0.00005193384,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001873741,"about_ca_topic_score_gemma":0.00000782078,"domain_scores_codex":[0.9995466,0.00006589853,0.0001529648,0.0001213545,0.00005151335,0.00006164659],"domain_scores_gemma":[0.9992936,0.00008172681,0.00005534418,0.0004139476,0.0001367118,0.00001869688],"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":[0.00002213784,0.00003472795,0.0000600975,0.0001162529,0.0001320704,4.953469e-8,0.00006959298,0.000001934022,0.9823491,0.0148538,0.0008274519,0.001532814],"study_design_scores_gemma":[0.0004499008,0.0004675389,0.0001639802,0.0002283205,0.00008295291,0.000006934084,0.0004524548,0.0009231344,0.9670331,0.00275009,0.02726189,0.0001796358],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6977808,0.2728106,0.02043495,0.00519433,0.0002304634,0.002930969,0.0002202531,0.00006421089,0.0003333817],"genre_scores_gemma":[0.9738654,0.001416613,0.02448284,0.00002634003,0.00001783114,0.00009488279,0.0000502803,0.000008330627,0.00003744218],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2760846,"threshold_uncertainty_score":0.2441621,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03666794119979606,"score_gpt":0.3280314413523073,"score_spread":0.2913635001525112,"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."}}