{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008502117,0.0001676072,0.0002070639,0.0002548103,0.0002206916,0.0004763483,0.0001787707,0.0002025531,0.0004960326],"category_scores_gemma":[0.0002745452,0.0001356153,0.0001183439,0.000259751,0.0002178595,0.0002356651,0.0001875415,0.0001868543,0.0001189301],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004875633,"about_ca_system_score_gemma":0.0002611166,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002082481,"about_ca_topic_score_gemma":0.002898099,"domain_scores_codex":[0.9998962,0.00001524041,0.000004488189,0.00003245469,0.00003108355,0.00002047798],"domain_scores_gemma":[0.9999266,0.00002490517,0.00001507666,0.000005007214,0.00001031102,0.00001816935],"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":[0.0002426752,0.00003602441,0.008125468,0.00004416262,0.00001902391,0.0000796732,0.00004699894,0.008775765,0.977383,0.0006915203,0.00006316527,0.004492661],"study_design_scores_gemma":[0.00003108438,0.0002859635,0.06854347,0.00001319574,0.00005893555,0.0003974108,0.0005653174,0.1731021,0.7525769,0.001816987,0.002565013,0.00004358298],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9966434,0.0001451152,0.002645564,0.00003220041,7.30797e-7,0.000002631478,0.00009906534,0.00003398179,0.0003973133],"genre_scores_gemma":[0.9981847,0.00008640866,0.001454237,0.00001676238,3.263124e-7,0.000003553725,0.0001171409,0.000006431535,0.0001302463],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002082481,"threshold_uncertainty_score":0.004140675,"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."}}