{"id":"W2109339916","doi":"10.1016/j.jmb.2011.10.003","title":"Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope","year":2011,"lang":"en","type":"article","venue":"Journal of Molecular Biology","topic":"Monoclonal and Polyclonal Antibodies Research","field":"Medicine","cited_by":103,"is_retracted":false,"has_abstract":false,"ca_institutions":"Princess Margaret Cancer Centre; Ontario Institute for Cancer Research; University of Toronto","funders":"National Research Council Canada; Western Economic Diversification Canada; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Canada Research Chairs; University of Saskatchewan; Canadian Light Source; International AIDS Vaccine Initiative","keywords":"Epitope; Scaffold; Side chain; Grafting; Chemistry; Linear epitope; Computational biology; Biology; Antigen; Computer science; Immunology","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":[],"consensus_categories":[],"category_scores_codex":[0.0007620228,0.0001345544,0.0006193761,0.0002019968,0.00003483764,0.000001994806,0.0002037786,0.0001430144,0.0002004947],"category_scores_gemma":[0.0002358865,0.00009916929,0.0002140587,0.0001796445,0.0002839725,0.00003321712,0.00007874759,0.0002189129,0.000007502292],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001895473,"about_ca_system_score_gemma":0.0002165836,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001502362,"about_ca_topic_score_gemma":8.525795e-7,"domain_scores_codex":[0.9982537,0.0003012118,0.000768597,0.000135541,0.0003116945,0.0002292516],"domain_scores_gemma":[0.9983042,0.000227504,0.0005371644,0.0001281676,0.0006485722,0.0001544012],"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":[0.002432901,0.0006819628,0.01218625,0.0001280881,0.0006105025,0.0002315065,0.0002331976,0.0004494224,0.9734616,0.001911584,0.0008511099,0.006821872],"study_design_scores_gemma":[0.004681532,0.009934213,0.0239731,0.0003478727,0.0002752275,0.00122344,0.0001012508,0.001740993,0.9466568,0.009530686,0.001232045,0.0003028477],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9459891,0.002165285,0.05081023,0.0005367053,0.0001149418,0.0001345053,0.00002652778,0.000003718528,0.0002189767],"genre_scores_gemma":[0.9350148,0.0003492604,0.06428784,0.0001728886,0.00009508614,0.000001140728,0.00001885507,0.00001315918,0.00004694088],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02680482,"threshold_uncertainty_score":0.4044006,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04512373220690105,"score_gpt":0.3245926485985136,"score_spread":0.2794689163916125,"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."}}