{"id":"W4408308366","doi":"10.1155/jna/5518018","title":"A Base Pair Outside the Catalytic Core of the I‐R3 DNA Enzyme Has a Significant Effect on Its Cleavage Activity: An Improved Catalytic Core Model and an Automated Design Program","year":2025,"lang":"en","type":"article","venue":"Journal of Nucleic Acids","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University; Concordia University","funders":"Concordia University","keywords":"Core (optical fiber); Cleavage (geology); Catalysis; DNA; Enzyme; Computer science; Combinatorial chemistry; Computational biology; Chemistry; Biology; Biochemistry","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":[],"consensus_categories":[],"category_scores_codex":[0.0007579401,0.0003265531,0.0004238495,0.00005347054,0.0002164308,0.00008613256,0.000688637,0.0002643975,0.000002064932],"category_scores_gemma":[0.0003122977,0.0001931054,0.0002192336,0.0001952389,0.0003614453,0.00003081568,0.0001793025,0.0004081138,7.623038e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005628777,"about_ca_system_score_gemma":0.0003919928,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001283574,"about_ca_topic_score_gemma":0.000007355484,"domain_scores_codex":[0.9984107,0.0001626773,0.0004522468,0.0003647387,0.0002817873,0.0003278775],"domain_scores_gemma":[0.9982929,0.00008662244,0.00048695,0.0007698092,0.0001791974,0.0001845324],"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":[0.001031586,0.0004433923,0.0005024227,0.0001162453,0.0001970113,0.00001836242,0.0001714034,0.0004658606,0.9900281,0.0000103525,0.001492625,0.005522573],"study_design_scores_gemma":[0.001350598,0.002875966,0.002045832,0.0001387761,0.0002763587,0.00008331847,0.0001569291,0.143778,0.8488722,0.00005620376,0.0001577656,0.0002081483],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982256,0.0001358516,0.00033182,0.0004093834,0.0001135118,0.0005821576,0.00003392771,0.00004114186,0.0001266399],"genre_scores_gemma":[0.9989714,0.00001807125,0.0004036406,0.0002746751,0.00008907934,0.00001902479,0.00001396516,0.0000415524,0.0001686177],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1433121,"threshold_uncertainty_score":0.787461,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03325541737476362,"score_gpt":0.3010605185544716,"score_spread":0.267805101179708,"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."}}