{"id":"W2081536974","doi":"10.1021/bi800355t","title":"The bZIP Targets Overlapping DNA Subsites within a Half-Site, Resulting in Increased Binding Affinities","year":2008,"lang":"en","type":"article","venue":"Biochemistry","topic":"Diffusion and Search Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Institute of General Medical Sciences","keywords":"bZIP domain; Affinities; Binding site; Leucine zipper; DNA; Zipper; Chemistry; DNA footprinting; Footprinting; Binding affinities; Stereochemistry; Biochemistry; DNA-binding protein; Peptide sequence; Transcription factor; Base sequence; 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":[0.0004217198,0.0002045092,0.0001529098,0.00004678231,0.0003903486,0.00006753192,0.0003086374,0.0001988535,0.000009460232],"category_scores_gemma":[0.0007844154,0.000172333,0.00009216271,0.0001742848,0.000224399,0.000006887599,0.0002122752,0.0002127221,0.00001096085],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003311435,"about_ca_system_score_gemma":0.0001964504,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001089187,"about_ca_topic_score_gemma":0.0001471048,"domain_scores_codex":[0.9985704,0.00006401583,0.0003223395,0.0003889621,0.0002327025,0.0004215322],"domain_scores_gemma":[0.9992002,0.0000772295,0.0001227172,0.0004075491,0.00007427188,0.0001179955],"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":[0.0001350034,0.00004980879,0.01448174,0.00002595441,0.00001929416,0.00003489699,0.0001850083,0.00001335227,0.9839561,0.00004301454,0.0009444967,0.0001113135],"study_design_scores_gemma":[0.001175127,0.00005826712,0.004163665,0.0000941658,0.000006961076,0.0001252591,0.001035737,0.001439864,0.9836853,0.00002337215,0.007755232,0.0004370653],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.994146,0.0007776832,0.00001701368,0.00009475342,0.00009891277,0.0001112596,0.00002761745,0.00002851666,0.004698197],"genre_scores_gemma":[0.9948955,0.0004075048,0.0003819188,0.0001176643,0.0001496164,0.00002106587,0.0002838109,0.000026527,0.003716413],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01031807,"threshold_uncertainty_score":0.7027536,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01360694704373278,"score_gpt":0.2357349977174197,"score_spread":0.222128050673687,"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."}}