{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001019807,0.0002488066,0.0002543959,0.0002239482,0.0002956325,0.0002601998,0.0002950134,0.0004303454,0.00173231],"category_scores_gemma":[0.0002149621,0.0002858497,0.0004044051,0.0001228099,0.0003055111,0.0002342568,0.0003539091,0.0004747696,0.0007803176],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003116528,"about_ca_system_score_gemma":0.0001949371,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003982268,"about_ca_topic_score_gemma":0.0008705341,"domain_scores_codex":[0.9998897,0.00001295674,0.000006066381,0.00003570224,0.00003746608,0.0000180324],"domain_scores_gemma":[0.9998453,0.00003256005,0.00004417327,0.00001645692,0.00001522314,0.00004619986],"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":[0.0001414502,0.00001586144,0.001125531,0.0000653587,0.000009469096,0.0000862007,0.00002977006,0.0001965532,0.9961576,0.00080117,0.0000636995,0.001307345],"study_design_scores_gemma":[0.00005164232,0.0002417362,0.07757606,0.0000316822,0.00003656654,0.001564812,0.0001184042,0.003819459,0.9066651,0.001176274,0.008685413,0.00003287549],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9854923,0.001972227,0.00879802,0.0001056684,0.00001717553,0.00002600394,0.0002727081,0.0001564586,0.003159448],"genre_scores_gemma":[0.99216,0.0003621014,0.005052214,0.000121504,0.000009435469,0.00002288615,0.0009037234,0.00003608581,0.001332045],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00173231,"threshold_uncertainty_score":0.005795181,"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."}}