{"id":"W4392399115","doi":"10.1039/d3cp06201e","title":"Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I-<i>Ppo</i>I","year":2024,"lang":"en","type":"article","venue":"Physical Chemistry Chemical Physics","topic":"Advanced biosensing and bioanalysis techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge","funders":"Natural Sciences and Engineering Research Council of Canada; Alliance de recherche numérique du Canada; Alberta Innovates; University of Lethbridge; Canada Research Chairs; Universities Space Research Association","keywords":"QM/MM; Phosphodiester bond; Chemistry; Catalysis; Metal; Deoxyribozyme; Stereochemistry; Substrate (aquarium); Homing endonuclease; Endonuclease; Computational chemistry; DNA; Combinatorial chemistry; Organic chemistry; Biochemistry; Biology; RNA","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":[0.0003697271,0.0003161152,0.0004978385,0.00008361357,0.0003028195,0.0005748034,0.0009708016,0.0008498216,0.001894128],"category_scores_gemma":[0.0005451444,0.0001811483,0.0003458157,0.0001303029,0.0004075594,0.0006972336,0.0002800243,0.001029136,0.0003434984],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004133336,"about_ca_system_score_gemma":0.0006671418,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001718484,"about_ca_topic_score_gemma":0.001333374,"domain_scores_codex":[0.9999411,0.000008008155,0.000003677866,0.00001506729,0.00001787537,0.00001420568],"domain_scores_gemma":[0.9998831,0.00005014683,0.00001546777,0.00002442316,0.00001657028,0.00001034451],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002447315,0.0002771554,0.005016807,0.001541587,0.0001388282,0.001632813,0.0006871362,0.3514294,0.4318081,0.1394777,0.002875267,0.06487058],"study_design_scores_gemma":[0.00003794292,0.0001767748,0.001232214,0.00003448561,0.00003269762,0.0003790052,0.000207083,0.8946456,0.08143067,0.01711082,0.004671793,0.00004094525],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.646993,0.001681441,0.3264893,0.00117563,0.0001399717,0.0001535148,0.000427729,0.0005563586,0.02238305],"genre_scores_gemma":[0.9426242,0.0009247372,0.05397806,0.0001265129,0.00001267526,0.00004116394,0.0001783063,0.00006402667,0.002050275],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001894128,"threshold_uncertainty_score":0.006336451,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02887778669827541,"score_gpt":0.2637809469007095,"score_spread":0.2349031602024341,"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."}}