{"id":"W2011721714","doi":"10.1021/bi050863a","title":"Transition State Structure of 5‘-Methylthioadenosine/<i>S</i>-Adenosylhomocysteine Nucleosidase from <i>Escherichia coli</i> and Its Similarity to Transition State Analogues","year":2005,"lang":"en","type":"article","venue":"Biochemistry","topic":"Biochemical and Molecular Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":108,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; Hospital for Sick Children","funders":"","keywords":"Chemistry; Kinetic isotope effect; Escherichia coli; Stereochemistry; Transition state; Dihedral angle; Nucleophile; Leaving group; Anomer; Catalysis; Ribose; Active site; Enzyme; Organic chemistry; Hydrogen bond; Molecule; Deuterium; Biochemistry","routes":{"ca_aff":true,"ca_fund":false,"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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0001160365,0.0003280367,0.0003198287,0.0000477442,0.0000841069,0.00003946535,0.0002533701,0.0003228495,0.00004953644],"category_scores_gemma":[0.00006291582,0.0003326641,0.000122483,0.0002054369,0.0001285988,0.00001303565,0.0001076317,0.0002629539,0.00000505856],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003017171,"about_ca_system_score_gemma":0.0000918778,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008092059,"about_ca_topic_score_gemma":0.00004489936,"domain_scores_codex":[0.9980913,0.00007961248,0.0003990237,0.0006974232,0.0003276766,0.0004049567],"domain_scores_gemma":[0.9989317,0.00001635272,0.0001017195,0.0003833437,0.0002126117,0.0003542857],"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":[0.0004966828,0.0001266552,0.00002195158,0.0001581956,0.00009223437,0.00000778078,0.0002526864,0.0001014632,0.9967059,0.000001732988,0.0009157062,0.001118951],"study_design_scores_gemma":[0.0009844321,0.0002122761,0.0003198185,0.00006107176,0.00004515114,0.000008120827,0.00005010345,0.0001942599,0.995739,0.0000675457,0.001951229,0.0003669868],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9921338,0.002826889,0.001205389,0.001418313,0.00003208508,0.0003239055,0.001982891,0.00002673282,0.00005000079],"genre_scores_gemma":[0.9952042,0.0003062525,0.001528149,0.001336164,0.0002432768,0.00001288497,0.001210857,0.00004215717,0.0001160656],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003070398,"threshold_uncertainty_score":0.9999126,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006666541592634843,"score_gpt":0.2371061346579117,"score_spread":0.2304395930652768,"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."}}