{"id":"W4416308130","doi":"10.1038/s41564-025-02179-1","title":"Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin","year":2025,"lang":"en","type":"article","venue":"Nature Microbiology","topic":"Clostridium difficile and Clostridium perfringens research","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":false,"ca_institutions":"SickKids Foundation; University of Toronto; Hospital for Sick Children","funders":"Hospital for Sick Children","keywords":"Cholic acid; Bile acid; Clostridium difficile toxin B; Chenodeoxycholic acid; Toxin; Virulence factor; Amino acid; Clostridioides; G protein-coupled bile acid receptor","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003557891,0.0004222244,0.0009649064,0.0006627285,0.0001219419,0.00002221496,0.0004003648,0.001269976,0.0005095263],"category_scores_gemma":[0.0007848539,0.0003353692,0.0002780582,0.0009342163,0.0004172505,0.00003956245,0.0002518443,0.001485359,0.00003778513],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002756352,"about_ca_system_score_gemma":0.0006452632,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000326408,"about_ca_topic_score_gemma":0.00001400898,"domain_scores_codex":[0.9974445,0.000263989,0.000600163,0.0007454212,0.0002121889,0.0007337291],"domain_scores_gemma":[0.9980592,0.0004522011,0.0001750488,0.0008004114,0.0003722699,0.000140835],"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":[0.0007103325,0.000250394,0.0007885743,0.0002551301,0.0002327236,0.00004040899,0.00006072729,0.0000279801,0.9720353,0.0003219066,0.02309544,0.002181056],"study_design_scores_gemma":[0.002072727,0.0004474681,0.0002827793,0.000319868,0.0001748683,0.0003205625,0.00009069252,0.00005144087,0.9880101,0.0001842368,0.007797996,0.0002472761],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9862852,0.007838329,0.0003874754,0.002045678,0.0006173475,0.001143152,0.0003262475,0.000112016,0.001244519],"genre_scores_gemma":[0.9963052,0.0002773963,0.00094518,0.0006896841,0.0001366271,0.00002731177,0.0002242679,0.00004059495,0.001353744],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01597476,"threshold_uncertainty_score":0.9999098,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02106529609111115,"score_gpt":0.3018810455713128,"score_spread":0.2808157494802017,"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."}}