{"id":"W4391759726","doi":"10.1109/tcbb.2024.3362308","title":"DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots","year":2024,"lang":"en","type":"article","venue":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta; University of Victoria","funders":"Western Canada Research Grid","keywords":"Nucleic acid; Pseudoknot; Duplex (building); Nucleic acid structure; Computational biology; Base pair; DNA; Nucleic acid secondary structure; RNA; Folding (DSP implementation); Biology; Computer science; Base sequence; Genetics; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004928863,0.0006201929,0.0008033434,0.0004893058,0.0006737896,0.0007620408,0.0009753616,0.0007496272,0.002498397],"category_scores_gemma":[0.001215576,0.0003138749,0.0005244476,0.0003324182,0.0004156408,0.0007811647,0.001033978,0.0004740043,0.0005484947],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006444295,"about_ca_system_score_gemma":0.001020456,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002467496,"about_ca_topic_score_gemma":0.007348244,"domain_scores_codex":[0.9995872,0.00006277056,0.00002813056,0.0001335209,0.0001394207,0.00004894267],"domain_scores_gemma":[0.9993681,0.0002280007,0.0001259655,0.00009787719,0.0001027585,0.00007722869],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.003923645,0.000430928,0.06956042,0.001434278,0.0003041239,0.001298727,0.0005328787,0.350322,0.1798091,0.02938398,0.01254474,0.3504552],"study_design_scores_gemma":[0.00004929788,0.0003088761,0.004276274,0.00003327616,0.00004139288,0.0005435615,0.0001150027,0.9351332,0.04187767,0.005657574,0.01190469,0.00005921621],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.3811346,0.0009778287,0.5995486,0.0001777369,0.000161698,0.0002506254,0.001704075,0.008951305,0.00709343],"genre_scores_gemma":[0.6601911,0.0001872641,0.3312742,0.0001324441,0.00001722007,0.0001194065,0.003605727,0.0005809339,0.003891751],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.002498397,"threshold_uncertainty_score":0.008357942,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01301600516026323,"score_gpt":0.2659151565292789,"score_spread":0.2528991513690157,"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."}}