{"id":"W4404917915","doi":"10.1101/2024.11.27.625581","title":"CycleDesigner: Leveraging RFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Chemical Synthesis and Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Tellabs (Canada)","funders":"","keywords":"Cyclic peptide; Peptide; Computer science; Chemistry; Biochemistry","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":[0.0005574121,0.0005922993,0.000554151,0.0002180695,0.0001686344,0.0002806223,0.000401531,0.0005550244,0.00001953956],"category_scores_gemma":[0.0001646569,0.0005929459,0.0003126271,0.0002467275,0.00007370149,0.000005352363,0.0008556578,0.0003292007,0.00002832535],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001078989,"about_ca_system_score_gemma":0.0001571698,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001852044,"about_ca_topic_score_gemma":0.000001191735,"domain_scores_codex":[0.9970756,0.00008827883,0.0004616593,0.001556451,0.0002432266,0.0005747643],"domain_scores_gemma":[0.9983574,0.00006373289,0.0001672877,0.0008591234,0.0001775607,0.0003748817],"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":[0.00006714559,0.00005980897,0.0001913247,0.0002197264,0.0002284055,0.0000101161,0.000006751573,0.0001154097,0.9943966,0.00006097529,0.004619022,0.00002469857],"study_design_scores_gemma":[0.0003195316,0.00007371599,0.001125488,0.0002669238,0.0001970743,2.598749e-8,0.000004371581,0.0004396269,0.9678257,0.00002021969,0.02891308,0.0008142676],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9544899,0.005308808,0.03777282,0.0006822473,0.000475965,0.0009647497,0.000164882,0.0001305156,0.00001006628],"genre_scores_gemma":[0.9800663,0.0009785083,0.01732942,0.0003045994,0.0008195646,0.0002940254,0.000002495801,0.0001687267,0.00003638494],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02657094,"threshold_uncertainty_score":0.9996522,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01678816459603113,"score_gpt":0.2215945670500138,"score_spread":0.2048064024539827,"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."}}