{"id":"W4311080423","doi":"10.21203/rs.3.rs-2327641/v1","title":"Molecular mechanism of phosphopeptide neoantigen immunogenicity","year":2022,"lang":"en","type":"preprint","venue":"Research Square","topic":"Monoclonal and Polyclonal Antibodies Research","field":"Medicine","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Brookhaven National Laboratory; Argonne National Laboratory; Basic Energy Sciences; National Institute of General Medical Sciences; National Institutes of Health; University of Chicago; Biological and Environmental Research; McMaster University; U.S. Department of Energy","keywords":"Phosphopeptide; Immunogenicity; T-cell receptor; Serine; Computational biology; Chemistry; Major histocompatibility complex; Ternary complex; Phosphorylation; Immune system; T cell; Cancer research; Biology; Biochemistry; Immunology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001763373,0.0002543547,0.0001624668,0.0001432916,0.0001674141,0.0004844455,0.0003457253,0.0003169188,0.003395843],"category_scores_gemma":[0.0001584856,0.0001309803,0.0002411937,0.00007056938,0.0002403595,0.0003960321,0.0003454756,0.0004516736,0.0009406122],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003152502,"about_ca_system_score_gemma":0.0001703189,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001146943,"about_ca_topic_score_gemma":0.00006965283,"domain_scores_codex":[0.9999025,0.00001490841,0.000004804229,0.00002068812,0.00003118098,0.00002586972],"domain_scores_gemma":[0.9999036,0.00001672361,0.00002498093,0.00001384233,0.000015684,0.00002513281],"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":[0.0002804705,0.00005983241,0.0006211706,0.00009397469,0.00001120456,0.000338685,0.00002509908,0.0007254855,0.9858877,0.005128058,0.0003519602,0.006476343],"study_design_scores_gemma":[0.00004721044,0.0002733909,0.002678654,0.000008432701,0.00001571929,0.0007556006,0.00003011831,0.007305312,0.9825232,0.001529933,0.004824058,0.000008474034],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9639096,0.003190853,0.01954472,0.0006360595,0.0001681614,0.00007742998,0.0001781643,0.0002809895,0.01201407],"genre_scores_gemma":[0.990765,0.0007728136,0.002560037,0.0001024786,0.0000331534,0.00002839227,0.0001371999,0.00002312934,0.005577838],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003395843,"threshold_uncertainty_score":0.01136029,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06746216333888895,"score_gpt":0.4172059748559483,"score_spread":0.3497438115170594,"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."}}