{"id":"W2165276671","doi":"10.1007/s00214-008-0440-9","title":"Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations","year":2008,"lang":"en","type":"article","venue":"Theoretical Chemistry Accounts","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":50,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; Deutsche Forschungsgemeinschaft; Western Canada Research Grid","keywords":"ReaxFF; Chemistry; Hydrogen bond; Molecular dynamics; RNA; Elongation; Active site; DNA; Polymerase; Crystallography; Stereochemistry; Biophysics; Computational chemistry; Molecule; Catalysis; Biochemistry; Materials science; Organic chemistry; Biology","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":[0.00004847072,0.0001313994,0.0001480075,0.000005480251,0.0001020033,0.000003616673,0.0001568073,0.0001750203,0.0001455514],"category_scores_gemma":[0.0000884012,0.00009622706,0.00006795535,0.00007389584,0.0008834088,0.000006096637,0.0001763341,0.00009249192,8.157897e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007742912,"about_ca_system_score_gemma":0.00004216125,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004564441,"about_ca_topic_score_gemma":1.413384e-7,"domain_scores_codex":[0.9992685,0.00001661863,0.0002062261,0.0002133391,0.0001556763,0.0001396093],"domain_scores_gemma":[0.99937,0.000009586645,0.000137393,0.0003347428,0.00008321428,0.00006501142],"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":[0.00009635302,0.00007505635,0.0008912425,0.00003556934,0.00002761015,4.783549e-7,0.00007809611,4.497584e-7,0.9984058,0.0001241806,0.0001179097,0.0001473266],"study_design_scores_gemma":[0.0003069133,0.00002044775,0.0031501,0.00002036552,0.00002575828,0.00002288082,0.00001848753,0.00002819669,0.9957201,0.00009452062,0.0004822196,0.00011004],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961908,0.0000486542,0.00006775375,0.0001202978,0.00002006932,0.00006526072,0.0004297023,0.000005529694,0.003051965],"genre_scores_gemma":[0.9987984,0.00006933219,0.00001683534,0.00005863809,0.00007316696,0.000004911392,0.0002436482,0.00001489401,0.0007201965],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002685658,"threshold_uncertainty_score":0.3924026,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.002921697233437707,"score_gpt":0.1937695216640635,"score_spread":0.1908478244306258,"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."}}