{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004587807,0.0002262113,0.0002764195,0.0002867842,0.0002821744,0.0001152435,0.0002577117,0.0001878001,0.00001780057],"category_scores_gemma":[0.0003332207,0.0002148171,0.0001899888,0.0007205991,0.0001296853,0.00005912431,0.0001525416,0.0001155687,0.00001653675],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000017857,"about_ca_system_score_gemma":0.00006433242,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007288959,"about_ca_topic_score_gemma":0.0007122841,"domain_scores_codex":[0.9983971,0.00007755992,0.0003833367,0.0005135843,0.0002797427,0.0003486456],"domain_scores_gemma":[0.9987603,0.00009012696,0.0001763939,0.0005557647,0.0002696665,0.0001476992],"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":[0.0001037745,0.00004795713,0.003046819,0.00005844455,0.0004674549,0.000005264417,0.0002187225,0.0002112005,0.993432,0.00002684355,0.0009377037,0.001443784],"study_design_scores_gemma":[0.001887385,0.0004527023,0.04351102,0.00008352747,0.0006543917,0.000008900372,0.0007510831,0.005013269,0.9289814,0.0004215997,0.0173838,0.0008508929],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961101,0.0006172347,0.002109108,0.0002041018,0.0000294152,0.0005584353,0.000245072,0.00005769622,0.0000688076],"genre_scores_gemma":[0.9899315,0.0006135633,0.0003870208,0.00008223913,0.00006112122,0.0002189724,0.008150037,0.00002908206,0.0005264163],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06445061,"threshold_uncertainty_score":0.8759989,"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."}}