{"id":"W2921184491","doi":"10.1371/journal.pcbi.1006845","title":"Predicting the mechanism and rate of H-NS binding to AT-rich DNA","year":2019,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":43,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"University of Toronto; Holland Research School of Molecular Chemistry; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Government of Ontario; Compute Canada","keywords":"DNA; Nucleoid; Biophysics; Binding site; HMG-box; Biology; DNA binding site; Chemistry; Crystallography; Biochemistry; DNA-binding protein; Escherichia coli; Transcription factor","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":[0.0001070922,0.00008167225,0.000102075,0.00001996172,0.00005827724,0.000004812565,0.000118131,0.00008496286,0.00003130718],"category_scores_gemma":[0.00005725757,0.00006224046,0.00002619833,0.00004924207,0.00004961094,0.000001422003,0.000204159,0.00004471519,0.00002198569],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007780519,"about_ca_system_score_gemma":0.0000235205,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002384793,"about_ca_topic_score_gemma":0.00000117567,"domain_scores_codex":[0.9994384,0.00003737488,0.000136677,0.0002182672,0.0000441607,0.0001251268],"domain_scores_gemma":[0.9996494,0.00007219814,0.00006914956,0.0001152134,0.00005619083,0.00003785177],"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":[0.00003231332,0.00001433503,0.01772183,0.00001450071,0.00005178867,2.243888e-7,0.00005624162,0.0001764795,0.9806227,0.001102192,0.0001048167,0.000102562],"study_design_scores_gemma":[0.0004003954,0.0002712615,0.005474747,0.00001469457,0.00001790772,0.00001726526,0.0000820301,0.001672417,0.9884401,0.002442706,0.001025928,0.0001405633],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984279,0.00005984526,0.0003491346,0.000314259,0.00007626692,0.0001212054,0.00003901392,0.000007359208,0.0006050751],"genre_scores_gemma":[0.9983952,0.000008918832,0.000720336,0.0003441735,0.00007020267,0.000007381337,0.0001419666,0.00000866466,0.0003031648],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01224709,"threshold_uncertainty_score":0.2538092,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00804649470205633,"score_gpt":0.2250564519811775,"score_spread":0.2170099572791212,"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."}}