{"id":"W2323760554","doi":"10.1021/bi1013547","title":"A Stereochemical Glimpse of the Active Site of the 8−17 Deoxyribozyme from Iodine-Mediated Cross-Links Formed with the Substrate’s Scissile Site","year":2010,"lang":"en","type":"article","venue":"Biochemistry","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Canadian Institutes of Health Research","keywords":"Deoxyribozyme; Phosphodiester bond; Scissile bond; Ribozyme; Hairpin ribozyme; Active site; Chemistry; Stereochemistry; Residue (chemistry); DNA; RNA; Cleavage (geology); VS ribozyme; Hammerhead ribozyme; Deoxyadenosine; Catalysis; Biochemistry; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001882779,0.0002651847,0.0002272758,0.000009984604,0.0001596681,0.00003434535,0.0008121032,0.0005852861,0.00008909584],"category_scores_gemma":[0.0002330119,0.000131383,0.0002258073,0.0001626351,0.0006959073,0.000006627626,0.000276076,0.0004580572,0.000003473708],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001172174,"about_ca_system_score_gemma":0.0002342887,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006538432,"about_ca_topic_score_gemma":0.0001103384,"domain_scores_codex":[0.9986216,0.00005416235,0.0003020847,0.0004027944,0.0003284239,0.000290955],"domain_scores_gemma":[0.99801,0.00008691617,0.0003976861,0.001225648,0.0001943261,0.00008542393],"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":[0.0003686231,0.00006568116,0.006803835,0.00002693936,0.00008068935,7.346456e-7,0.0001208386,0.000001804878,0.9918398,0.000005773662,0.0005154833,0.000169835],"study_design_scores_gemma":[0.0006168606,0.00005207357,0.01074018,0.00004970913,0.00005539973,0.00001187933,0.0001018136,0.00001369695,0.9872421,0.00006146078,0.0008719116,0.0001828899],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9977771,0.0001789885,0.00003084453,0.0004119023,0.0001261062,0.0003201495,0.000630093,0.000009411911,0.0005153778],"genre_scores_gemma":[0.9986787,0.000009849347,0.0001689563,0.0001581923,0.0002052831,0.00004299095,0.0001335474,0.00002693694,0.0005755745],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00459764,"threshold_uncertainty_score":0.5357645,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005833536381572763,"score_gpt":0.2220409121114776,"score_spread":0.2162073757299048,"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."}}