{"id":"W4411370530","doi":"10.1021/acsphyschemau.5c00033","title":"Understanding the Binding and Structures in Model Complexes of Polypeptides and Cofactors","year":2025,"lang":"en","type":"article","venue":"ACS Physical Chemistry Au","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Windsor; York University","funders":"NIH Clinical Center; Natural Sciences and Engineering Research Council of Canada; Alliance de recherche numérique du Canada; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; University of Windsor; Radboud Universiteit; Research Grants Council, University Grants Committee; Department of Science and Technology of Shandong Province; Shandong University","keywords":"Cofactor; Chemistry; Biophysics; Computational biology; Stereochemistry; Biochemistry; Biology; Enzyme","routes":{"ca_aff":true,"ca_fund":true,"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":[0.00003684306,0.00009815891,0.0001197969,0.00001121298,0.00006011213,0.00001336696,0.00009264208,0.00006892792,4.570858e-7],"category_scores_gemma":[0.00003357329,0.00007295892,0.00002400128,0.00006196939,0.0002260925,0.00000319968,0.0001264983,0.00008826191,2.001859e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001844231,"about_ca_system_score_gemma":0.00004242605,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001935326,"about_ca_topic_score_gemma":0.00001199953,"domain_scores_codex":[0.9995602,0.000009196189,0.00009155644,0.0001680461,0.00005253456,0.0001184536],"domain_scores_gemma":[0.9997621,0.00002828108,0.00003772479,0.0001375856,0.00001054106,0.00002372906],"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":[0.00002380634,0.000008279945,0.003873436,0.00006571128,0.00002250105,2.364343e-7,0.0001020394,0.0004103886,0.9921859,0.003145631,0.00001713726,0.0001449447],"study_design_scores_gemma":[0.0002769606,0.00001563289,0.00277087,0.00002549853,0.00001664722,0.00000238512,0.0003108293,0.003754441,0.9611754,0.03153067,0.00001716791,0.0001035247],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9973882,0.0001173487,0.001515554,0.00006980015,0.000007673743,0.00005646031,0.0000180215,0.000003251742,0.0008236883],"genre_scores_gemma":[0.9997445,0.00002210556,0.00007885237,0.00003548753,0.0000326648,0.000002732732,0.00001715649,0.000005085092,0.00006141049],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03101051,"threshold_uncertainty_score":0.2975178,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02106006638787798,"score_gpt":0.2649166623161772,"score_spread":0.2438565959282992,"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."}}