{"id":"W3185978387","doi":"10.26434/chemrxiv.10316177.v1","title":"Computational Approach Choice in Modeling Flexible Enzyme Active Sites","year":2019,"lang":"en","type":"preprint","venue":"ChemRxiv","topic":"Enzyme Catalysis and Immobilization","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Windsor","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Sulfenic acid; Chemistry; Nucleophile; Sulfonium; Substrate (aquarium); ONIOM; Stereochemistry; Molecule; Computational chemistry; Catalysis; Enzyme; Salt (chemistry); Organic chemistry; Cysteine","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":[0.0001429244,0.0002395561,0.0002674862,0.00009396514,0.00003181422,0.00004178514,0.0002609168,0.0004167674,0.00001609035],"category_scores_gemma":[0.00008288647,0.0002540114,0.0001408535,0.0001111408,0.00003161605,0.000005639453,0.0004030492,0.0002812422,0.00001479162],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004764167,"about_ca_system_score_gemma":0.0001521896,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003018778,"about_ca_topic_score_gemma":0.000007378821,"domain_scores_codex":[0.9986531,0.00003791118,0.0002757357,0.0006852738,0.0001469116,0.0002010338],"domain_scores_gemma":[0.99923,0.00001482833,0.0001269104,0.0004402912,0.0001430421,0.00004496471],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00002610058,0.0001192929,0.002106702,0.0001380922,0.00006599084,2.495833e-7,0.0000703322,0.9124171,0.08440338,0.00003807129,0.0004956644,0.0001190774],"study_design_scores_gemma":[0.000571635,0.00003390769,0.0009427976,0.00006366742,0.00003627215,0.000002202606,0.00007881047,0.7320127,0.2646346,0.0003644423,0.0007665419,0.0004923357],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9269589,0.001214853,0.06848333,0.00003090201,0.0001172701,0.0003428923,0.00001437348,0.00001986425,0.002817606],"genre_scores_gemma":[0.9892464,0.00008183836,0.00181961,0.0001128945,0.000241446,0.00006944804,0.007727568,0.0000369,0.0006639297],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1804043,"threshold_uncertainty_score":0.9999912,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02949947071008206,"score_gpt":0.2776532630371321,"score_spread":0.2481537923270501,"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."}}