{"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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":["insufficient_payload"],"category_scores_codex":[0.0006871361,0.0002584787,0.000364224,0.0002971418,0.0004425756,0.00009459903,0.0003548416,0.0004148579,0.004043219],"category_scores_gemma":[0.0002503763,0.0002180156,0.00006662056,0.0003515292,0.0007915331,0.000304909,0.0002652753,0.001188124,0.002005723],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002225503,"about_ca_system_score_gemma":0.0002165248,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009496013,"about_ca_topic_score_gemma":0.0002593074,"domain_scores_codex":[0.997136,0.0006668092,0.0002527435,0.0006771046,0.0002905664,0.0009767504],"domain_scores_gemma":[0.9986313,0.0003699308,0.00008103871,0.0004826752,0.0002575394,0.000177541],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000344729,0.0001396196,0.2012324,0.0001035182,0.0002422107,0.00005594753,0.00108182,0.000001759488,0.7301437,0.0002497323,0.04561868,0.02078587],"study_design_scores_gemma":[0.007506086,0.001557521,0.7999646,0.0001493994,0.00003092561,0.00008895884,0.005399406,0.0001340656,0.06321142,0.0007539158,0.1205046,0.0006991461],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9893122,0.004019417,0.000009663601,0.0004527136,0.0001381083,0.0007919666,0.001147737,0.00006337856,0.004064816],"genre_scores_gemma":[0.9895239,0.0002141959,0.0001357234,0.0001462367,0.00001902205,0.00004343706,0.0008426054,0.00003913534,0.009035676],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6669323,"threshold_uncertainty_score":0.9987713,"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."}}