{"id":"W4211062370","doi":"10.1101/gad.348993.121","title":"Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins","year":2022,"lang":"en","type":"article","venue":"Genes & Development","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Institute of Neurological Disorders and Stroke; National Institute of General Medical Sciences; National Science Foundation; National Institutes of Health; National Cancer Institute; Chinese Academy of Medical Sciences; National Natural Science Foundation of China","keywords":"Biology; DNA; DNA-binding domain; Repressor; Genetics; DNA-binding protein; Computational biology; HMG-box; Binding domain; DNA binding site; Binding site; Plasma protein binding; Protein domain; DNA sequencing; Gene; Cell biology; Transcription factor; Promoter; Gene expression","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":[0.00018904,0.0001972882,0.0001376283,0.00003624306,0.0005754216,0.00004239635,0.000304735,0.00005387964,0.00009919363],"category_scores_gemma":[0.000005972593,0.0002025112,0.00006950845,0.00007205365,0.00003472419,0.000002546336,0.00030626,0.0000594616,0.000004169622],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000140509,"about_ca_system_score_gemma":0.0001828528,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006429819,"about_ca_topic_score_gemma":0.0000337961,"domain_scores_codex":[0.9987411,0.00003590633,0.0002732202,0.0004199037,0.000173051,0.0003568571],"domain_scores_gemma":[0.9995304,0.000006574189,0.0001119386,0.0002353414,0.00003698262,0.00007881408],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00005486783,0.00002910914,0.001569281,0.0000304727,0.00005436486,0.000004181363,0.0002034694,0.00007787099,0.978314,0.0001424384,0.004393271,0.01512661],"study_design_scores_gemma":[0.0005463882,0.0001667162,0.001417997,0.000004924578,0.000007124682,0.00002942671,0.0004783914,0.00008289104,0.2524674,0.000193403,0.7441784,0.000427008],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9959614,0.000460653,0.00201864,0.0001474306,0.0002607382,0.0005794247,0.0004614663,0.00001487441,0.0000953443],"genre_scores_gemma":[0.9563683,0.00003687265,0.03798699,0.0001164293,0.0001175648,0.000594261,0.003633114,0.00004353462,0.001102913],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7397851,"threshold_uncertainty_score":0.8258166,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0141228444456222,"score_gpt":0.2283014629651222,"score_spread":0.2141786185195,"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."}}