{"id":"W4387497936","doi":"10.1021/acscatal.3c02378","title":"Human <i>O</i>-GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics","year":2023,"lang":"en","type":"article","venue":"ACS Catalysis","topic":"Glycosylation and Glycoproteins Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Agència de Gestió d'Ajuts Universitaris i de Recerca; Biotechnology and Biological Sciences Research Council; Canadian Institutes of Health Research; Ministerio de Ciencia e Innovación; H2020 European Research Council; Agencia Estatal de Investigación; Ministerio de Ciencia, Innovación y Universidades; Canada Research Chairs; Royal Society; Diamond Light Source","keywords":"Chemistry; Metadynamics; Glycosidic bond; Stereochemistry; Substrate (aquarium); QM/MM; Catalysis; Active site; Enzyme; Protein structure; Biochemistry; Molecular dynamics; Computational chemistry; 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":[0.000344951,0.0005212377,0.0004264537,0.00005822859,0.0003414698,0.0006490397,0.0008315718,0.0004914405,0.00152918],"category_scores_gemma":[0.0002878667,0.0002988447,0.0003728257,0.0001401232,0.0004761783,0.0005019468,0.0003319735,0.001002231,0.0003679712],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007299574,"about_ca_system_score_gemma":0.0007765768,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002740576,"about_ca_topic_score_gemma":0.002671399,"domain_scores_codex":[0.9999076,0.00001830599,0.000004387015,0.00002355153,0.00002666968,0.00001938736],"domain_scores_gemma":[0.9999429,0.0000140402,0.00001141506,0.00001273022,0.000008610099,0.00001026402],"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":[0.0008193424,0.0003432131,0.01111555,0.0007158784,0.0003462119,0.0009212045,0.0003477917,0.09991782,0.8035606,0.04004644,0.004696873,0.03716925],"study_design_scores_gemma":[0.0005567012,0.000848253,0.008033963,0.00007474428,0.0001695365,0.0007966153,0.0002800841,0.5809335,0.3781827,0.01225893,0.01769849,0.000166517],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8980123,0.001401401,0.08667083,0.0008205689,0.0001170181,0.00007849119,0.0004901285,0.0009463878,0.01146287],"genre_scores_gemma":[0.9776112,0.0009990936,0.01881266,0.0002172438,0.000009496839,0.00004874366,0.0007294529,0.0001229419,0.001449349],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002740576,"threshold_uncertainty_score":0.005449235,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03208133929469294,"score_gpt":0.3072193904231109,"score_spread":0.2751380511284179,"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."}}