{"id":"W2029633855","doi":"10.1016/j.molimm.2008.07.020","title":"A novel computer algorithm improves antibody epitope prediction using affinity-selected mimotopes: A case study using monoclonal antibodies against the West Nile virus E protein","year":2008,"lang":"en","type":"article","venue":"Molecular Immunology","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":false,"ca_institutions":"McMaster University","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health","keywords":"Mimotope; Epitope; Monoclonal antibody; Linear epitope; Epitope mapping; Antibody; Phage display; Computational biology; Biology; Virology; Immunology","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":[0.0002508355,0.0004329938,0.000403456,0.0001381809,0.0007698566,0.00008258744,0.0004005847,0.0002785742,0.000004565577],"category_scores_gemma":[0.00005333261,0.0003544728,0.0001680428,0.0003455155,0.0002488604,0.00003025541,0.0005140523,0.0003660511,0.000004454068],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004704372,"about_ca_system_score_gemma":0.0002274187,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001042525,"about_ca_topic_score_gemma":0.00004029008,"domain_scores_codex":[0.997884,0.0002242361,0.000629931,0.0005185452,0.0001868283,0.0005564998],"domain_scores_gemma":[0.9985927,0.00001498445,0.0002980073,0.0007451559,0.0002926896,0.00005642223],"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":[0.00007554547,0.0006702869,0.0006347083,0.0000161192,0.0005737973,0.0003973035,0.0006878815,0.0007455542,0.9935945,0.000003629207,0.00001388106,0.002586752],"study_design_scores_gemma":[0.005449396,0.003325168,0.01269348,0.00007306637,0.0002603049,0.02661038,0.003874753,0.1932206,0.7522916,0.000007102146,0.000917831,0.0012763],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9306521,0.001367477,0.06627446,0.00002228755,0.0002402249,0.001323997,0.00005714257,0.00004408936,0.0000181456],"genre_scores_gemma":[0.9721733,0.000126768,0.02701826,0.000119603,0.0001841732,0.00006409369,0.0002305905,0.00006276135,0.00002048274],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.241303,"threshold_uncertainty_score":0.9998907,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0212166594406956,"score_gpt":0.2545168093126561,"score_spread":0.2333001498719605,"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."}}