{"id":"W3112873140","doi":"10.1093/nar/gkaa1021","title":"PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins","year":2020,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":153,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children; University of Toronto","funders":"National Institutes of Health; European Commission; Universidad Nacional de Quilmes; Horizon 2020 Framework Programme; National Institute of General Medical Sciences; Vrije Universiteit Brussel; Hungarian Scientific Research Fund; Ministero dell’Istruzione, dell’Università e della Ricerca; Consejo Nacional de Investigaciones Científicas y Técnicas; Fondation pour la Recherche Médicale; Agencia Nacional de Promoción Científica y Tecnológica; Agence Nationale de la Recherche; Natural Sciences and Engineering Research Council of Canada; Leukaemia and Blood Cancer New Zealand","keywords":"Biology; Computational biology; Intrinsically disordered proteins; Database; Biochemistry; Computer science","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":[0.0004915234,0.0001303131,0.0001783997,0.00005099826,0.000105908,0.00002527362,0.0006416065,0.0001540677,0.00003557593],"category_scores_gemma":[0.001092977,0.00009718148,0.00009111142,0.0004080212,0.0002058525,0.000007098484,0.0006596699,0.0003358605,0.000008048117],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001765969,"about_ca_system_score_gemma":0.0002648363,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005641485,"about_ca_topic_score_gemma":0.0001959447,"domain_scores_codex":[0.9983613,0.0001998667,0.0002584033,0.0004199203,0.0003541663,0.0004063709],"domain_scores_gemma":[0.9990349,0.00002131495,0.00006142242,0.0005718984,0.0002071128,0.0001033064],"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":[0.0007475876,0.00006499059,0.0006631248,0.000138014,0.00002151947,0.000002779532,0.00009735097,0.000007621247,0.990495,0.001265265,0.0008155447,0.005681217],"study_design_scores_gemma":[0.002690147,0.000987572,0.001649642,0.00007475584,0.000009958058,0.000003107902,0.0001926322,0.001574676,0.9498041,0.0028269,0.03991462,0.0002718804],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9863699,0.0002163986,0.005298015,0.004559334,0.00002444189,0.002870324,0.0001693759,0.000006688474,0.0004855337],"genre_scores_gemma":[0.9931908,0.00003432382,0.005705598,0.0001725413,0.0001583225,0.0003539649,0.00009427393,0.00003029965,0.0002598424],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04069088,"threshold_uncertainty_score":0.3962946,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02460760496791055,"score_gpt":0.3082780048254721,"score_spread":0.2836703998575616,"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."}}