{"id":"W4392860407","doi":"10.1101/2024.03.14.585084","title":"A random mutagenesis screen enriched for missense mutations in bacterial effector proteins","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Legionella and Acanthamoeba research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary; University of Toronto","funders":"","keywords":"Effector; Biology; Saccharomyces cerevisiae; Mutagenesis; Genetics; Legionella pneumophila; In silico; Computational biology; Mutant; Cell biology; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0007328618,0.0005069932,0.0005224352,0.0003043748,0.0001222002,0.0002322841,0.000452868,0.0007355777,0.00002737759],"category_scores_gemma":[0.0006023757,0.0005114418,0.0003094297,0.000336401,0.0001234155,0.000006131047,0.0006232766,0.0004854145,0.00004510665],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001165906,"about_ca_system_score_gemma":0.0009877717,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001935037,"about_ca_topic_score_gemma":0.0000369814,"domain_scores_codex":[0.9972123,0.0002309098,0.0004835129,0.00117802,0.0002642919,0.0006309755],"domain_scores_gemma":[0.9982763,0.00008140285,0.0001574852,0.000886423,0.0003656458,0.0002327403],"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":[0.0005878765,0.0001278829,0.0003730333,0.0008509738,0.0002118743,0.00007855203,0.000008275206,0.00004621123,0.9971834,0.00004504046,0.000482572,0.000004237225],"study_design_scores_gemma":[0.003647927,0.0002184339,0.006615793,0.0003698542,0.0001519645,8.025188e-8,0.000003557373,0.0004070528,0.9798439,0.000007505061,0.007865276,0.0008687001],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9920969,0.00157243,0.001254733,0.0002493423,0.0007554524,0.003034485,0.0009418572,0.0000881998,0.000006624255],"genre_scores_gemma":[0.9934707,0.0001481078,0.002801183,0.00005972504,0.00138183,0.001902084,0.00001988721,0.0001718259,0.00004470225],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01733962,"threshold_uncertainty_score":0.9997337,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01321072916288864,"score_gpt":0.2536769881435114,"score_spread":0.2404662589806227,"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."}}