{"id":"W2999559717","doi":"10.1093/nar/gkz1164","title":"Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure","year":2019,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":55,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; National Institutes of Health","keywords":"Biology; Deamination; Cytidine deaminase; Genetics; Retrotransposon; DNA; Mutagenesis; Context (archaeology); Oligonucleotide; Mutation; Enzyme; Biochemistry; Gene; Genome","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":[0.0001513181,0.0001826503,0.0001914129,0.0002722989,0.00025346,0.0002449924,0.000117697,0.0002863319,0.0007783581],"category_scores_gemma":[0.0002231126,0.0001249405,0.0001386134,0.0002074938,0.0001838343,0.000142329,0.0001538304,0.0002226109,0.0002562721],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001604378,"about_ca_system_score_gemma":0.0001324996,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006324252,"about_ca_topic_score_gemma":0.001247592,"domain_scores_codex":[0.9998092,0.00003106665,0.00001117609,0.00006667726,0.00005410525,0.00002771602],"domain_scores_gemma":[0.9997347,0.00006047797,0.000091612,0.00001841026,0.00004223529,0.00005254031],"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":[0.00005549618,0.000007769146,0.00206313,0.00001225656,0.000005381725,0.00002945062,0.00001843739,0.00003377957,0.9958298,0.00003575153,0.000009662055,0.001899244],"study_design_scores_gemma":[0.000008360146,0.0004233465,0.0779113,0.000008944203,0.00003103693,0.001053589,0.0001172078,0.001139117,0.9172458,0.000208653,0.001839359,0.00001330015],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9962483,0.0007711547,0.002135168,0.00001395611,0.000003836246,0.000009255652,0.00006080512,0.00003301928,0.0007243955],"genre_scores_gemma":[0.9973616,0.0002051934,0.001841139,0.00001916043,0.00000251057,0.000007058884,0.0001114183,0.000009943579,0.0004418972],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007783581,"threshold_uncertainty_score":0.002603829,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01901168778689324,"score_gpt":0.2853733028306131,"score_spread":0.2663616150437199,"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."}}