{"id":"W4220898305","doi":"10.1016/j.xpro.2022.101271","title":"Evaluation of Jumonji C lysine demethylase substrate preference to guide identification of in vitro substrates","year":2022,"lang":"en","type":"article","venue":"STAR Protocols","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Carleton University","funders":"","keywords":"Lysine; Substrate (aquarium); Demethylase; In vitro; Biochemistry; Enzyme; Identification (biology); Methyltransferase; Computational biology; Methylation; Chemistry; Biology; Amino acid; Epigenetics; Botany; Gene","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":[0.002821845,0.00009074745,0.0001397999,0.0001041924,0.00003754168,0.000008378056,0.0001823794,0.00004568636,0.00004623195],"category_scores_gemma":[0.0002508578,0.00009902318,0.00004418813,0.0002661973,0.00002627279,0.000004783552,0.00007989918,0.00005803168,0.000001123394],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004606516,"about_ca_system_score_gemma":0.000250013,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006247597,"about_ca_topic_score_gemma":0.00006674458,"domain_scores_codex":[0.9981835,0.0003676224,0.0005538513,0.0002632341,0.000505501,0.0001263163],"domain_scores_gemma":[0.9988779,0.00001304231,0.0002798622,0.0003354848,0.0004588118,0.00003494004],"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":[0.000175202,0.0001210033,0.002216967,0.00003305161,0.00001358157,1.788253e-7,0.00008783474,0.006830828,0.9849071,0.0000200365,0.00001916963,0.005575031],"study_design_scores_gemma":[0.0005963492,0.0003371778,0.02100658,0.00001033686,0.00001864919,2.002894e-7,0.00007918197,0.0007752876,0.9755158,0.0007636456,0.0008044279,0.00009236905],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9795418,0.0001411209,0.0005542433,0.00002618561,0.00002157591,0.01938747,0.00007878254,0.000003003324,0.0002458136],"genre_scores_gemma":[0.9688945,0.000005852504,0.0008428589,0.000006623703,0.00001741549,0.02999385,0.0001545921,0.00001072144,0.00007360237],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01878962,"threshold_uncertainty_score":0.4038048,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06688334117322067,"score_gpt":0.3621449013884133,"score_spread":0.2952615602151927,"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."}}