{"id":"W2104151407","doi":"10.1016/j.str.2005.11.017","title":"Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes","year":2006,"lang":"en","type":"article","venue":"Structure","topic":"DNA Repair Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Alberta","funders":"Canadian Institutes of Health Research; Alberta Heritage Foundation for Medical Research; Canada Research Chairs","keywords":"DNA; Steric effects; Hydrogen bond; Transcription factor; Crystallography; Protein–DNA interaction; Saccharomyces cerevisiae; Base pair; Chemistry; Consensus sequence; Gene; Transcription (linguistics); Protein Data Bank (RCSB PDB); Binding site; DNA-binding protein; DNA binding site; Promoter; Genetics; Stereochemistry; Biology; Biochemistry; Gene expression; Base sequence; Molecule","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002101993,0.0003054165,0.0002478782,0.0002082843,0.0004308991,0.0005930199,0.0004216404,0.0003710871,0.0008317917],"category_scores_gemma":[0.0003034096,0.0002636756,0.0002046596,0.0001462217,0.0008241581,0.0004786827,0.0001680308,0.0008393848,0.0003617373],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004837259,"about_ca_system_score_gemma":0.0003580367,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006629372,"about_ca_topic_score_gemma":0.0009464077,"domain_scores_codex":[0.9999382,0.000008988884,0.00000385411,0.00001352325,0.00002457793,0.00001087495],"domain_scores_gemma":[0.9998823,0.00003995638,0.00002265189,0.00001900597,0.00001562032,0.00002046356],"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":[0.0001292325,0.00006898308,0.001046463,0.0001131503,0.00001946659,0.000199832,0.0001824913,0.003561439,0.9758151,0.01338868,0.0001433167,0.005331822],"study_design_scores_gemma":[0.000045325,0.0003621383,0.01287695,0.00003386385,0.00005315798,0.001569964,0.0002959538,0.03822089,0.9171065,0.02320023,0.006172718,0.00006223023],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.947966,0.001464483,0.04511019,0.0004501214,0.00002768748,0.00005955471,0.000103971,0.0001773569,0.004640583],"genre_scores_gemma":[0.9887751,0.0005794954,0.009245245,0.00006713869,0.000006253679,0.00003077264,0.0000887899,0.00001694771,0.001190211],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0008317917,"threshold_uncertainty_score":0.003509641,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01129266949234973,"score_gpt":0.2380770557100416,"score_spread":0.2267843862176919,"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."}}