{"id":"W4413991818","doi":"10.1002/prot.70043","title":"Functional Relevance of <scp>CASP16</scp> Nucleic Acid Predictions as Evaluated by Structure Providers","year":2025,"lang":"en","type":"article","venue":"Proteins Structure Function and Bioinformatics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"York University","funders":"Office of Research Infrastructure Programs, National Institutes of Health; National Key Research and Development Program of China; Leibniz-Gemeinschaft; Natural Sciences and Engineering Research Council of Canada; Stanford Bio-X; Office of Science; National Institutes of Health; Novo Nordisk Fonden; National Natural Science Foundation of China; Deutsche Forschungsgemeinschaft; Argonne National Laboratory; Aarhus Universitet; European Commission; U.S. Department of Energy; National Institute of Allergy and Infectious Diseases; Howard Hughes Medical Institute; Villum Fonden; National Institute of General Medical Sciences; Novo Nordisk; Common Fund; Gottfried Wilhelm Leibniz Universität Hannover; National Science Foundation","keywords":"Nucleic acid; Nucleic acid structure; Computational biology; Protein secondary structure; Structural motif; RNA; Base pair; DNA; Nucleic acid secondary structure; Chemistry; Biological system; Biology; Biochemistry","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":[0.0001420617,0.0002874293,0.0002397254,0.0001319111,0.0002603775,0.00006497479,0.0001488896,0.0004003655,0.00009449211],"category_scores_gemma":[0.0004647578,0.0002411954,0.00009031032,0.0002824622,0.0001457633,0.00003870292,0.00009660508,0.0002007669,0.000004679174],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002472951,"about_ca_system_score_gemma":0.0001813209,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001142954,"about_ca_topic_score_gemma":0.00001378309,"domain_scores_codex":[0.9985778,0.00006115416,0.0004843897,0.000300745,0.0003103882,0.0002654666],"domain_scores_gemma":[0.9989825,0.00002871431,0.0002890811,0.0003603379,0.0002412748,0.00009811371],"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":[0.0001486213,0.00002868285,0.0002582085,0.0002809426,0.0001893078,1.725792e-7,0.00008458349,0.0001194639,0.9686896,0.0009004225,0.01199765,0.0173023],"study_design_scores_gemma":[0.001239111,0.0008959042,0.001151926,0.00009073947,0.0001497113,0.00003329851,0.0004756043,0.002318468,0.936828,0.006340337,0.05030464,0.000172245],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7044788,0.003150969,0.2827433,0.0005006696,0.001601939,0.002881216,0.0009388158,0.0001529403,0.003551363],"genre_scores_gemma":[0.9902154,0.0001761911,0.006332689,0.0006158403,0.0001205945,0.000057894,0.0005727718,0.00002410459,0.001884557],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2857366,"threshold_uncertainty_score":0.9835663,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005747314496420494,"score_gpt":0.2132509857266848,"score_spread":0.2075036712302643,"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."}}