{"id":"W7139674991","doi":"","title":"De Novo Design of Cyclic Peptide Binders Using Generative Models","year":2025,"lang":"","type":"dissertation","venue":"TSpace (University of Toronto)","topic":"Chemical Synthesis and Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Amgen (Canada)","funders":"","keywords":"Cyclic peptide; Peptide; Benchmark (surveying); Monte Carlo method; Offset (computer science); Markov chain Monte Carlo; Markov chain","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":[0.0006898367,0.0007342642,0.0009620984,0.0004490837,0.0003553424,0.000730879,0.001042639,0.001116976,0.003672839],"category_scores_gemma":[0.001937485,0.0008611948,0.001195039,0.0004197475,0.0007940899,0.0006103034,0.0009835684,0.00114517,0.000606612],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001252975,"about_ca_system_score_gemma":0.001599856,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003955043,"about_ca_topic_score_gemma":0.006200507,"domain_scores_codex":[0.9997221,0.0000607274,0.00001076391,0.00006176961,0.00009368474,0.00005101037],"domain_scores_gemma":[0.9989007,0.0007596709,0.00008419587,0.00007548557,0.0001101787,0.00006989515],"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":[0.00004716095,0.00004277048,0.0003552795,0.00004054911,0.000017639,0.00005770241,0.00002509117,0.9712971,0.002557331,0.007851881,0.000638977,0.01706852],"study_design_scores_gemma":[0.000008422442,0.00001861246,0.00001857397,0.000002377749,0.000003906265,0.00000612841,0.000003193702,0.9975157,0.000427554,0.001649579,0.0003440995,0.000001941043],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1281475,0.0007280945,0.8512139,0.0004835648,0.0001067602,0.0001662525,0.0002241272,0.001849365,0.0170805],"genre_scores_gemma":[0.7195884,0.0004237677,0.2701538,0.0003677631,0.00004521327,0.0002852461,0.0004842566,0.0004679341,0.008183657],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.003955043,"threshold_uncertainty_score":0.01228684,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02605543441065479,"score_gpt":0.257575479073344,"score_spread":0.2315200446626892,"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."}}