{"id":"W2622435197","doi":"10.1038/s41598-017-03298-4","title":"Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily","year":2017,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":30,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université du Québec; Université Laval; PROTEO; Institut National de la Recherche Scientifique","funders":"National Institute of General Medical Sciences; Fonds de Recherche du Québec - Santé; Oak Ridge National Laboratory; Universitaire Stichting; University of Texas Southwestern Medical Center; Natural Sciences and Engineering Research Council of Canada; McGill University; National Institutes of Health","keywords":"Protein superfamily; Ribonuclease; Amino acid; Computational biology; Biology; RNase P; Peptide sequence; SUPERFAMILY; Function (biology); Conserved sequence; Genetics; Sequence (biology); RNA; Gene","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":[0.0005110968,0.0001509051,0.0001392764,0.0000433491,0.0005031373,0.0004136397,0.0002354244,0.0001488632,0.0000144464],"category_scores_gemma":[0.0001034808,0.0001243359,0.00006720126,0.00004528738,0.000436012,0.00003044887,0.0001933002,0.0001032924,0.000002127833],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001374025,"about_ca_system_score_gemma":0.0001180101,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005798486,"about_ca_topic_score_gemma":0.0004575295,"domain_scores_codex":[0.9984735,0.00003922067,0.0002926049,0.0006986149,0.000202344,0.0002936664],"domain_scores_gemma":[0.9982001,0.000001388395,0.0001847788,0.001399958,0.0001165022,0.00009725634],"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":[0.00005835987,0.00002883286,0.04703429,0.0000090354,0.00001421519,0.0001035969,0.00003339056,0.001994835,0.9486664,0.00002596215,0.0006610716,0.001370027],"study_design_scores_gemma":[0.0006282976,0.0001907335,0.2578292,0.00005995978,0.00002418711,0.0003493674,0.00007742957,0.01730797,0.7102066,0.003213257,0.009415443,0.0006976256],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9943964,0.0004605186,0.001338211,0.000057694,0.002973341,0.0002174824,0.000003356447,0.00001433784,0.0005386852],"genre_scores_gemma":[0.997094,0.000008080632,0.0002139671,0.00005266412,0.0001986861,0.00002545547,0.0002467549,0.0000153834,0.002145055],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2384598,"threshold_uncertainty_score":0.507027,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01977665324631004,"score_gpt":0.2375822765314344,"score_spread":0.2178056232851243,"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."}}