{"id":"W4323067007","doi":"10.1261/rna.079148.122","title":"Computational design and experimental verification of pseudoknotted ribozymes","year":2023,"lang":"en","type":"article","venue":"RNA","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Concordia University; Armand Frappier Museum; Institut National de la Recherche Scientifique","funders":"Fonds de recherche du Québec – Nature et technologies; Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; Armand-Frappier Foundation","keywords":"Pseudoknot; Ribozyme; Biology; Computational biology; RNA; Nucleic acid structure; Stem-loop; Base pair; Ligase ribozyme; Structural motif; Riboswitch; Synthetic biology; Nucleic acid secondary structure; Genetics; Non-coding RNA; Gene; 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":[0.0000946137,0.00004113766,0.00004519156,0.0000205202,0.00002706049,0.000004825375,0.00003956803,0.00003816777,0.00001388612],"category_scores_gemma":[0.00001537591,0.00004045697,0.00001601891,0.0000423477,0.00002383349,0.000001359045,0.00001995874,0.000009900322,0.000009101704],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000001880382,"about_ca_system_score_gemma":0.00001282462,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002001604,"about_ca_topic_score_gemma":5.931703e-8,"domain_scores_codex":[0.9996842,0.00003317499,0.00007009086,0.000101918,0.00005517246,0.00005541936],"domain_scores_gemma":[0.9998533,0.00001008307,0.00002968425,0.00007056269,0.0000176133,0.00001881083],"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":[0.00002955738,0.00001074958,0.00003519932,0.000004186665,0.000009653617,3.540571e-7,0.00003704466,0.0005047417,0.9968977,0.0002736782,0.0005282707,0.001668854],"study_design_scores_gemma":[0.0001187267,0.00008609543,0.0008230977,0.000004364624,0.000002472348,0.000002035543,0.00004457815,0.00120493,0.996819,0.0004181972,0.000430479,0.00004603659],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9752664,0.0003088765,0.02407138,0.00005796273,0.00003584626,0.0001002032,0.000004468703,0.00001115461,0.0001436994],"genre_scores_gemma":[0.9934301,0.00002925066,0.006287402,0.00002441701,0.00002587773,0.00001461058,0.00004345264,0.000006111082,0.0001387418],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01816373,"threshold_uncertainty_score":0.1649787,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02017542229606374,"score_gpt":0.2660041005076068,"score_spread":0.2458286782115431,"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."}}