{"id":"W2034766212","doi":"10.3390/molecules191015735","title":"A Multi-Scale Computational Study on the Mechanism of Streptococcus pneumoniae Nicotinamidase (SpNic)","year":2014,"lang":"en","type":"article","venue":"Molecules","topic":"Adenosine and Purinergic Signaling","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Windsor","funders":"Natural Sciences and Engineering Research Council of Canada; Compute Canada","keywords":"ONIOM; Thioester; Chemistry; Molecular mechanics; Density functional theory; Computational chemistry; Hydrolysis; Molecular dynamics; Stereochemistry; Enzyme; Active site; NAD+ kinase; Enzyme catalysis; Reaction mechanism; Phosphonate; Catalysis; Combinatorial chemistry; Organic chemistry","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":[0.0001819831,0.0001269633,0.0001170315,0.00002639171,0.00007668899,0.00001295629,0.0001979712,0.00005260783,0.00001676523],"category_scores_gemma":[0.00005960522,0.00009129519,0.00007375382,0.00005650145,0.00004448711,0.000001261484,0.00008886315,0.00007145777,0.00001001976],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003790156,"about_ca_system_score_gemma":0.00002085514,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001332812,"about_ca_topic_score_gemma":0.000007200328,"domain_scores_codex":[0.9991572,0.0001342681,0.0001803213,0.0002406678,0.0001536185,0.0001338762],"domain_scores_gemma":[0.9994768,0.00004451514,0.00008953966,0.0002845145,0.00006768092,0.00003693438],"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":[0.0000589574,0.001063402,0.006632476,0.00001654427,0.0001347159,0.000005827577,0.0004165419,0.01048192,0.9752173,0.003871257,0.001589055,0.0005119385],"study_design_scores_gemma":[0.004100595,0.004781617,0.05260171,0.00008139722,0.000130043,0.00001387728,0.002346992,0.04639295,0.8837326,0.002417938,0.002550414,0.0008498199],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.960345,0.00007230358,0.03873128,0.0001630845,0.0000340085,0.0002682844,0.00001139817,0.00000992889,0.0003646986],"genre_scores_gemma":[0.998715,0.000001944822,0.0007265058,0.000257325,0.00006552631,0.0000324922,0.00002805706,0.00001654804,0.0001565608],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09148472,"threshold_uncertainty_score":0.372291,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01461816600531152,"score_gpt":0.2551333987890321,"score_spread":0.2405152327837206,"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."}}