{"id":"W4416997207","doi":"10.1021/acs.biochem.5c00381","title":"Applications of KinTek Explorer Kinetic Simulations of Targeted Protein Degradation for Evaluation and Design of PROTACs","year":2025,"lang":"en","type":"article","venue":"Biochemistry","topic":"Protein Degradation and Inhibitors","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Discovery Centre","funders":"","keywords":"Ternary complex; Context (archaeology); Kinetic energy; Ternary operation; Mechanism (biology); Degradation (telecommunications); Protein degradation; Ubiquitin","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":[0.0004428981,0.0006120524,0.0008483475,0.000362612,0.0005537125,0.0006729548,0.0008567958,0.001025271,0.002743476],"category_scores_gemma":[0.001463302,0.0003168357,0.0004980778,0.0004046234,0.0004297882,0.0006161806,0.0005423395,0.0008980441,0.0002330552],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001230788,"about_ca_system_score_gemma":0.001416664,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007966381,"about_ca_topic_score_gemma":0.00557113,"domain_scores_codex":[0.9998685,0.00003778193,0.000008047812,0.00001708703,0.0000340289,0.00003448796],"domain_scores_gemma":[0.9992431,0.0005263539,0.00004938838,0.0000390559,0.00007771477,0.00006432846],"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":[0.0001247453,0.00008478036,0.001342838,0.00006652062,0.00002413152,0.0001145141,0.00007601285,0.9857071,0.003518401,0.006433111,0.0005963817,0.001911403],"study_design_scores_gemma":[0.00001710881,0.00001832992,0.00009820254,0.000003284625,0.000002443428,0.000005974242,0.00001835047,0.9983478,0.000627336,0.0005386431,0.0003181089,0.000004412702],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9219214,0.0004973688,0.0510515,0.0008073825,0.00008057582,0.0001136816,0.001361971,0.0007229421,0.02344326],"genre_scores_gemma":[0.9766955,0.0002382158,0.02044752,0.000107687,0.000008629301,0.000230557,0.0005286994,0.00012999,0.0016132],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007966381,"threshold_uncertainty_score":0.01583999,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01759950947347269,"score_gpt":0.2908570186865659,"score_spread":0.2732575092130933,"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."}}