{"id":"W3036325859","doi":"10.1101/2020.06.22.165571","title":"High-throughput binding affinity measurements for mutations spanning a transcription factor-DNA interface reveal affinity and specificity determinants","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Canadian Institutes of Health Research; Chemistry, Engineering and Medicine for Human Health, Stanford University; Alfred P. Sloan Foundation; National Science Foundation","keywords":"Transcription factor; DNA; Biology; Genetics; Mutant; Gene; Oligonucleotide; DNA binding site; Binding site; DNA sequencing; DNA-binding protein; Mutation; Computational biology; Promoter; Gene expression","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000291447,0.0003784672,0.0002972829,0.0002762424,0.0002956291,0.0003945115,0.0004623058,0.0004872527,0.001528783],"category_scores_gemma":[0.0004448686,0.0002370551,0.0002130372,0.0002074423,0.0003489808,0.0002950288,0.0002864177,0.0008518992,0.0005520528],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006307077,"about_ca_system_score_gemma":0.0002170381,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00119226,"about_ca_topic_score_gemma":0.002191,"domain_scores_codex":[0.9995986,0.00003105021,0.00002207488,0.0001241179,0.000164148,0.00006009565],"domain_scores_gemma":[0.9996663,0.0001217575,0.00007831226,0.00004798656,0.00004090639,0.0000447843],"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":[0.00002566565,0.00001453143,0.0009684473,0.00001287032,0.000007120647,0.00001247375,0.00001145503,0.0002576347,0.9973462,0.00009619633,0.00008702441,0.001160302],"study_design_scores_gemma":[0.000002374894,0.00002915229,0.002782349,0.00000120456,0.000004868646,0.00004579372,0.00001246449,0.002690485,0.993845,0.0000965797,0.0004836767,0.000006200989],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9664893,0.0004472285,0.03064465,0.0001417673,0.00002879986,0.00001677032,0.0006610047,0.000443621,0.001126863],"genre_scores_gemma":[0.9893638,0.0001218219,0.009117835,0.00004928648,0.000004296677,0.0000290418,0.0002531855,0.00003635932,0.00102447],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001528783,"threshold_uncertainty_score":0.005114257,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04182744343202348,"score_gpt":0.2905888410853286,"score_spread":0.2487613976533051,"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."}}