{"id":"W4320486808","doi":"10.1002/cpz1.661","title":"Pseudoknots in RNA Structure Prediction","year":2023,"lang":"en","type":"review","venue":"Current Protocols","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"","keywords":"Pseudoknot; RNA; Computational biology; Nucleic acid structure; Computer science; Nucleic acid secondary structure; Function (biology); Biology; Genetics; Gene","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":[0.0002869613,0.0004268246,0.0007834603,0.0001606284,0.00004889217,0.00005120994,0.0004586905,0.0005861112,0.00004877881],"category_scores_gemma":[0.0001284032,0.0003536973,0.0003123571,0.0002676874,0.00002949619,0.000003998988,0.0001849786,0.0003400684,0.00008987104],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004501691,"about_ca_system_score_gemma":0.0002703413,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001356771,"about_ca_topic_score_gemma":0.0000055012,"domain_scores_codex":[0.9979141,0.0002483071,0.0006156209,0.0006691546,0.0002091042,0.000343751],"domain_scores_gemma":[0.998939,0.000017439,0.0003020762,0.0006188187,0.00003788937,0.00008473619],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00001162172,0.00003812087,0.000004429981,0.0132043,0.00003819657,0.000003175106,0.000005414014,9.38454e-7,0.0009520205,0.00005152964,0.001438423,0.9842519],"study_design_scores_gemma":[0.0002070845,0.0001151326,0.000003183946,0.01550778,0.00005014834,0.000008783951,0.000001354218,0.000001193137,0.001604855,0.0002524498,0.9819334,0.0003146275],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.000008049516,0.9020408,0.0001314169,0.000003277542,0.0004615065,0.09685217,0.0003508824,0.00004653295,0.0001054098],"genre_scores_gemma":[0.0000022157,0.8084445,0.00007320756,0.00000428634,0.0007150495,0.1898151,0.000584678,0.00008186629,0.0002790929],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9839372,"threshold_uncertainty_score":0.9998915,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1027608634894581,"score_gpt":0.4057780087949539,"score_spread":0.3030171453054957,"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."}}