{"id":"W4405769055","doi":"10.1021/acs.jpcb.4c05875","title":"How Can One Metal Power Nucleic Acid Phosphodiester Bond Cleavage by a Nuclease? Multiscale Computational Studies Highlight a Diverse Mechanistic Landscape","year":2024,"lang":"en","type":"review","venue":"The Journal of Physical Chemistry B","topic":"Advanced biosensing and bioanalysis techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs; Alberta Innovates; Alberta Innovates - Technology Futures; University of Lethbridge","keywords":"Phosphodiester bond; Nuclease; Nucleic acid; Chemistry; Nucleophile; Bond cleavage; Combinatorial chemistry; Molecular mechanics; Stereochemistry; Cleavage (geology); DNA; Molecular dynamics; RNA; Biochemistry; Computational chemistry; Catalysis; Biology","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":[0.0005175055,0.0006032881,0.001319892,0.0003668066,0.0008027079,0.002090946,0.001367959,0.002292713,0.002965399],"category_scores_gemma":[0.001466741,0.0005730448,0.0009928817,0.0003166953,0.001344799,0.002642093,0.001131046,0.0009988163,0.0004118267],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000902472,"about_ca_system_score_gemma":0.0009098961,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004277339,"about_ca_topic_score_gemma":0.002934597,"domain_scores_codex":[0.9998493,0.00003859349,0.000006293913,0.00003609308,0.00002818056,0.00004148738],"domain_scores_gemma":[0.9997529,0.0001457017,0.00002110604,0.00002781343,0.00001877396,0.00003359404],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001377193,0.00009937889,0.003343851,0.0003748718,0.0001585377,0.0004486735,0.0001602111,0.8915663,0.009455623,0.08306188,0.001395289,0.009797702],"study_design_scores_gemma":[0.00005561795,0.00006342466,0.0004740483,0.0000269144,0.00005466223,0.0000491602,0.0001030247,0.9658729,0.001066747,0.02997349,0.002233453,0.00002654481],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"review","genre_scores_codex":[0.8431802,0.00315423,0.1076199,0.007417618,0.0003738097,0.0001060912,0.000562618,0.0004983835,0.03708707],"genre_scores_gemma":[0.9850332,0.001531325,0.01126168,0.0003399578,0.00004575581,0.00008491208,0.0001441164,0.00008035259,0.001478672],"genre_candidate":"review","genre_consensus":null,"teacher_disagreement_score":0.004277339,"threshold_uncertainty_score":0.009920239,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02046563710024121,"score_gpt":0.3020173932458066,"score_spread":0.2815517561455654,"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."}}