{"id":"W4406798116","doi":"10.1016/j.cell.2025.01.003","title":"Ligand interaction landscape of transcription factors and essential enzymes in E. coli","year":2025,"lang":"en","type":"article","venue":"Cell","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University; University of Regina; Ontario Institute for Cancer Research; University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Biology; Transcription factor; Transcription (linguistics); Enzyme; Computational biology; Genetics; Cell biology; Biochemistry; Gene","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":[0.00003623213,0.00004432526,0.00005867305,0.00004643411,0.000008481937,0.000004384367,0.00002014659,0.00005074983,0.000002906045],"category_scores_gemma":[0.000007924126,0.00003991196,0.00001720201,0.00005058328,0.00001186135,0.000001946948,0.000007588504,0.00003035039,2.011396e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000001967527,"about_ca_system_score_gemma":0.000007712772,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002730495,"about_ca_topic_score_gemma":0.00002086596,"domain_scores_codex":[0.9997551,0.000008649788,0.00007678609,0.00009811424,0.00001571792,0.00004564374],"domain_scores_gemma":[0.9999071,0.000001140113,0.0000167713,0.00005406734,0.00001271157,0.000008208764],"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":[0.00002581592,0.00002378489,0.001833889,0.00004834757,0.000004713526,6.136639e-8,0.00005019486,0.00003898695,0.997483,0.00001785603,0.0002570791,0.0002162404],"study_design_scores_gemma":[0.0002108979,0.00002511878,0.008102011,0.00001356116,0.000007387902,4.472169e-7,0.0000739559,0.00002114731,0.985731,0.000004444243,0.005774896,0.0000351304],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975771,0.001397363,0.0003463199,0.00002304075,0.0002860686,0.0000449867,0.000002630214,0.000003171388,0.0003192913],"genre_scores_gemma":[0.9991412,0.0003176326,0.00003382066,0.000006678844,0.00004709719,0.000001255512,0.00002308842,0.000002515708,0.000426784],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01175203,"threshold_uncertainty_score":0.1627563,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003981311887740261,"score_gpt":0.2112059112483835,"score_spread":0.2072245993606433,"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."}}