{"id":"W3200667584","doi":"10.1101/2021.09.23.461501","title":"Mechanism of the CBM35 domain in assisting catalysis by Ape1, a <i>Campylobacter jejuni</i> O-acetyl esterase","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Enzyme Structure and Function","field":"Materials Science","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Basic Energy Sciences; National Institute of General Medical Sciences; Biological and Environmental Research; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Office of Science; National Institutes of Health; SLAC National Accelerator Laboratory; University of British Columbia; U.S. Department of Energy","keywords":"Active site; Hydrolase; Campylobacter jejuni; Catalytic triad; Acetylation; Peptidoglycan; Stereochemistry; Biochemistry; Esterase; Chemistry; Docking (animal); Glycoside hydrolase; Campylobacter; Site-directed mutagenesis; Mutagenesis; Enzyme; Biology; Bacteria; Mutant","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0009899458,0.0005379265,0.0007587686,0.0001702185,0.0001745854,0.0002976546,0.000847153,0.0005485651,0.0001766206],"category_scores_gemma":[0.0002483075,0.0004611179,0.000251032,0.0008062011,0.0001460704,0.000233082,0.0009201399,0.000706461,0.0000156658],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002821581,"about_ca_system_score_gemma":0.0005245967,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003217947,"about_ca_topic_score_gemma":0.00006142572,"domain_scores_codex":[0.9965695,0.0004029194,0.0008178636,0.001085385,0.0005679567,0.0005564073],"domain_scores_gemma":[0.9969493,0.00008764683,0.0007696892,0.001733841,0.0003140623,0.0001454831],"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":[0.00001793744,0.0001066237,0.001624059,0.0002605101,0.00004302919,0.00002043977,0.00004521803,0.00004237178,0.9972883,0.0003409222,0.0002094866,0.000001061712],"study_design_scores_gemma":[0.0004197526,0.00002680886,0.006446208,0.0005106032,0.0001160295,5.471613e-8,0.00002470313,0.00005068064,0.9911581,0.0000122537,0.0007148432,0.0005199924],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9941983,0.0004362765,0.002145662,0.000167885,0.002162069,0.0004631494,0.0002787203,0.0001199223,0.00002805257],"genre_scores_gemma":[0.9947699,0.0000373217,0.004473822,0.0002945361,0.0002180942,0.0001133243,0.000001493514,0.00008159473,0.000009858985],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006130271,"threshold_uncertainty_score":0.9997841,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006788479180345944,"score_gpt":0.1910548484514871,"score_spread":0.1842663692711411,"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."}}