{"id":"W2015115438","doi":"10.1073/pnas.0911566106","title":"The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor","year":2009,"lang":"en","type":"article","venue":"Proceedings of the National Academy of Sciences","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":111,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Canadian Institutes of Health Research","keywords":"TetR; Allosteric regulation; Cooperativity; Repressor; Cooperative binding; Folding (DSP implementation); Allosteric enzyme; Biophysics; Chemistry; DNA; Plasma protein binding; Binding site; Biology; Biochemistry; Transcription factor; Gene; Receptor","routes":{"ca_aff":true,"ca_fund":true,"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":[0.001562695,0.00006469758,0.00009614445,0.00003638702,0.0002085516,0.00001359746,0.0005156823,0.00007677091,4.879008e-7],"category_scores_gemma":[0.001148833,0.00003199195,0.00005306939,0.0003090926,0.0006826985,0.00002468157,0.000091286,0.00009019829,3.282689e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006048832,"about_ca_system_score_gemma":0.0000280283,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001620615,"about_ca_topic_score_gemma":7.65788e-8,"domain_scores_codex":[0.9990834,0.00001957624,0.0002596918,0.0001477649,0.0004031176,0.00008642763],"domain_scores_gemma":[0.9992111,0.0000951977,0.0004622281,0.00001817231,0.0002013747,0.00001196503],"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":[0.000118719,0.00001497866,0.0009567341,0.000007711797,0.00001136679,8.886709e-10,0.00007469957,0.00004714583,0.996627,0.001250423,0.0002012604,0.000689953],"study_design_scores_gemma":[0.00009782667,0.0001333426,0.02208038,0.00002908725,0.000007394991,0.000003973094,0.0001210653,0.0001458028,0.9740522,0.003128674,0.0001631677,0.00003711604],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9966028,0.0004071685,0.000006264565,0.002556689,0.00001591056,0.0001358847,0.00001478135,0.000001348733,0.0002591874],"genre_scores_gemma":[0.999306,0.000132776,0.0003355299,0.00007604926,0.00003894686,0.000002710768,3.050471e-7,0.000001853438,0.0001058428],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02257484,"threshold_uncertainty_score":0.2515431,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01676787135976457,"score_gpt":0.2957409795294397,"score_spread":0.2789731081696752,"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."}}