{"id":"W4296191256","doi":"10.1101/2022.09.16.508321","title":"Computational remodeling of an enzyme conformational landscape for altered substrate selectivity","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Enzyme Structure and Function","field":"Materials Science","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"","keywords":"Substrate (aquarium); Selectivity; Chemistry; Conformational change; Enzyme; Kinetics; Biophysics; Structural plasticity; Substrate specificity; Molecular dynamics; Conformational ensembles; Catalysis; Stereochemistry; Computational chemistry; Biochemistry; Biology; Physics","routes":{"ca_aff":true,"ca_fund":false,"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":[0.000991435,0.000323976,0.0004450637,0.0002023406,0.0002786463,0.0001417754,0.0004008589,0.0002400059,0.0003424861],"category_scores_gemma":[0.00009803589,0.0003559432,0.0001261675,0.0002204885,0.00006822716,0.0003648734,0.0001863372,0.0003747846,0.00000705411],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001308517,"about_ca_system_score_gemma":0.000853655,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003520641,"about_ca_topic_score_gemma":0.0000032549,"domain_scores_codex":[0.9977838,0.0001388614,0.0006143174,0.0006356427,0.0004877849,0.0003395329],"domain_scores_gemma":[0.9979233,0.0001216921,0.0006274055,0.0005042782,0.0006965949,0.0001267827],"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":[0.0001847299,0.00009327107,0.0005541757,0.0003923895,0.0000483759,0.000001638752,0.00003281037,0.140883,0.8551995,0.002308883,0.0002995042,0.000001688583],"study_design_scores_gemma":[0.001379924,0.0002590882,0.0330272,0.0001065835,0.0001368963,9.872919e-8,0.00001584022,0.200987,0.7617205,0.0002549963,0.001179617,0.0009321869],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.958535,0.0001246726,0.03741394,0.00003656936,0.001604919,0.0006031115,0.001468289,0.0001955694,0.00001790794],"genre_scores_gemma":[0.9715751,0.000006119592,0.02762335,0.000084802,0.0004833219,0.0001589617,0.00001468945,0.0000513659,0.000002329996],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09347897,"threshold_uncertainty_score":0.9998893,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01736276270251931,"score_gpt":0.2369697248928663,"score_spread":0.219606962190347,"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."}}