{"id":"W4417277204","doi":"10.1093/bib/bbaf631.049","title":"Nativeness-constrained diffusion framework for nanobody design","year":2025,"lang":"en","type":"article","venue":"Briefings in Bioinformatics","topic":"Monoclonal and Polyclonal Antibodies Research","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Novelis (Canada)","funders":"","keywords":"Sequence (biology); Protein design; Generative model; Generative grammar; Epitope; Protein sequencing","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008661539,0.0006840592,0.000768569,0.0006632048,0.0004452577,0.0009219434,0.001231144,0.001512467,0.004578022],"category_scores_gemma":[0.001277733,0.0005417149,0.0009916428,0.0003593452,0.001188315,0.0008791885,0.00104188,0.0009862041,0.0004676422],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001842697,"about_ca_system_score_gemma":0.001150817,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005607345,"about_ca_topic_score_gemma":0.004251411,"domain_scores_codex":[0.999746,0.00009214571,0.000008594262,0.00004509892,0.00007561476,0.00003257129],"domain_scores_gemma":[0.9996142,0.0002145412,0.00003801844,0.00002045113,0.00006852207,0.00004420625],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0000160222,0.00001401274,0.0001281836,0.00003339299,0.00001149666,0.00004427082,0.00003162623,0.9338116,0.001199569,0.05974899,0.0004791669,0.004481737],"study_design_scores_gemma":[0.000004568325,0.000005739086,0.00001158077,0.00000270346,0.000001761349,0.000004751435,0.000002250781,0.9904142,0.00009835025,0.008923061,0.0005289344,0.000002180092],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01752725,0.0007561732,0.9691367,0.0007115329,0.00005459395,0.00004472799,0.00009861666,0.0002398128,0.01143059],"genre_scores_gemma":[0.7205439,0.0008215361,0.2568551,0.0003391952,0.00006982164,0.0003443024,0.0002100573,0.000245236,0.02057076],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.005607345,"threshold_uncertainty_score":0.015315,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03886001245050656,"score_gpt":0.3603519381875238,"score_spread":0.3214919257370172,"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."}}