{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004300803,0.0001577048,0.0003239663,0.0002837497,0.0001296401,0.00003860007,0.0001415948,0.0001668383,0.00004639223],"category_scores_gemma":[0.0008969491,0.0001272464,0.0001055187,0.0004365503,0.0001525978,0.00009878796,0.00008623242,0.0002635847,0.00001827497],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008113364,"about_ca_system_score_gemma":0.0002654845,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005621745,"about_ca_topic_score_gemma":0.000003162248,"domain_scores_codex":[0.9987637,0.00002100193,0.0004665327,0.0001363514,0.000251701,0.0003607475],"domain_scores_gemma":[0.9987105,0.0008076227,0.00007977316,0.0001799668,0.0001440142,0.00007817682],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004551807,0.0009300584,0.01585259,0.006504382,0.0003495317,0.00006259912,0.004505082,0.0001514468,0.005302048,0.6377893,0.02164901,0.3023521],"study_design_scores_gemma":[0.01378721,0.001848191,0.05272065,0.00929096,0.0002137756,0.0001838461,0.002077615,0.3433669,0.04308741,0.2485723,0.2835052,0.001346024],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.05586278,0.0003881536,0.9113873,0.014329,0.0002953375,0.002066004,0.00004398644,0.0001021384,0.01552534],"genre_scores_gemma":[0.1410728,0.0004149065,0.8413016,0.01150176,0.0001226142,0.0001909346,0.00009635184,0.00002822869,0.005270808],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.389217,"threshold_uncertainty_score":0.5188957,"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."}}