{"id":"W4399946649","doi":"10.1016/j.jim.2024.113713","title":"ERAMER: A novel in silico tool for prediction of ERAP1 enzyme trimming","year":2024,"lang":"en","type":"article","venue":"Journal of Immunological Methods","topic":"Peptidase Inhibition and Analysis","field":"Medicine","cited_by":3,"is_retracted":false,"has_abstract":false,"ca_institutions":"McMaster University","funders":"","keywords":"Trimming; In silico; Endoplasmic reticulum; Transporter associated with antigen processing; Antigen processing; Enzyme; MHC class I; Major histocompatibility complex; Antigen presentation; Golgi apparatus; Biochemistry; Cleavage (geology); Chemistry; Computational biology; Biology; Cell biology; Computer science; Gene; Cytotoxic T cell","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":[],"consensus_categories":[],"category_scores_codex":[0.0021241,0.0001013726,0.0005289785,0.0004496426,0.00002176656,0.00001839213,0.00006989703,0.0001449555,0.0001389221],"category_scores_gemma":[0.002290933,0.00006649842,0.0004749501,0.000449561,0.0000670803,0.0001142895,0.0000187025,0.0004453708,0.000001236487],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008710455,"about_ca_system_score_gemma":0.00009583253,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002667755,"about_ca_topic_score_gemma":1.349948e-7,"domain_scores_codex":[0.9985331,0.0001717301,0.0008519723,0.0001253612,0.0001726996,0.0001451161],"domain_scores_gemma":[0.9985142,0.0009560378,0.0002081324,0.0001013835,0.0001759213,0.00004436556],"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":[0.0004928448,0.0003028005,0.0002466702,0.00009610453,0.000219191,0.00003175284,0.0001144566,0.00002380782,0.8737858,0.000459543,0.0001291488,0.1240979],"study_design_scores_gemma":[0.0120598,0.009502552,0.08347698,0.01103988,0.00133202,0.002091173,0.001534201,0.02452105,0.8072452,0.005077137,0.04165699,0.000463057],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5156061,0.004379945,0.4776989,0.001666364,0.0001940664,0.0001857502,0.00003005606,0.00002612427,0.0002127181],"genre_scores_gemma":[0.6245129,0.0002591312,0.3745737,0.0001946534,0.0002017454,0.00001052401,0.000005117385,0.00001060022,0.0002316452],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1236349,"threshold_uncertainty_score":0.2742627,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07084399556985414,"score_gpt":0.4149770050856744,"score_spread":0.3441330095158203,"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."}}