{"id":"W2071477149","doi":"10.1002/prot.21876","title":"The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation","year":2008,"lang":"en","type":"article","venue":"Proteins Structure Function and Bioinformatics","topic":"Cancer therapeutics and mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Canada Research Chairs; McGill University","keywords":"Topoisomerase; DNA supercoil; DNA; Catalytic cycle; Molecular dynamics; DNA replication; Biophysics; Biology; Chemistry; Biochemistry; Enzyme; Computational 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004228113,0.0004971398,0.0008962965,0.0005869058,0.0007504452,0.0008096089,0.001293135,0.001408389,0.002489567],"category_scores_gemma":[0.001432962,0.0004362404,0.0009303967,0.0006181104,0.0007737251,0.0006438531,0.0006267635,0.0009111293,0.000251388],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001339802,"about_ca_system_score_gemma":0.001784406,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02982896,"about_ca_topic_score_gemma":0.01057404,"domain_scores_codex":[0.9998606,0.00004580052,0.000004811511,0.00002255707,0.00003539835,0.00003082915],"domain_scores_gemma":[0.9994186,0.0003190672,0.00003842045,0.00003764451,0.0001122677,0.00007409778],"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":[0.00005234744,0.00006865793,0.001303665,0.00003851758,0.00002991453,0.00006203834,0.00004799134,0.9889847,0.0008873295,0.005944916,0.0005240592,0.002055815],"study_design_scores_gemma":[0.000009195564,0.000006191918,0.000150916,0.000001804283,0.000001844152,0.000003411177,0.000007062133,0.9988754,0.00005922843,0.0007212435,0.0001611572,0.00000253953],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8564224,0.0008649022,0.1116482,0.001535265,0.0001626382,0.0002978566,0.001236165,0.0005682606,0.02726433],"genre_scores_gemma":[0.9431628,0.0004426515,0.05071936,0.0001634339,0.00004304594,0.0004740754,0.0008943811,0.0001145857,0.003985711],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02982896,"threshold_uncertainty_score":0.05931067,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004764150007974097,"score_gpt":0.2301495545687746,"score_spread":0.2253854045608006,"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."}}