{"id":"W2278226114","doi":"10.1504/ijbra.2015.071938","title":"A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures","year":2015,"lang":"en","type":"article","venue":"International Journal of Bioinformatics Research and Applications","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; Trinity Western University; Western University","funders":"","keywords":"Algorithm; Pseudoknot; Simulated annealing; Computer science; RNA; Nucleic acid secondary structure; Permutation (music); Biology; Physics; 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":[],"consensus_categories":[],"category_scores_codex":[0.0007820984,0.00008555855,0.00009923415,0.0002838722,0.00008733525,0.0001254008,0.0003529601,0.00007986377,0.000014984],"category_scores_gemma":[0.0002377961,0.00007378113,0.00004301832,0.0001551649,0.00006256501,0.00002581087,0.00008858941,0.0001559304,0.000008481955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003748958,"about_ca_system_score_gemma":0.0003144892,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000082235,"about_ca_topic_score_gemma":0.000001835542,"domain_scores_codex":[0.9987024,0.00005008656,0.0003829799,0.00009902682,0.000606722,0.0001587669],"domain_scores_gemma":[0.9978547,0.00005276024,0.0001580529,0.0001366268,0.0015337,0.000264126],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0006510314,0.0001849681,0.0001996456,0.00004837627,0.0003401266,0.00001413297,0.0007746589,0.009619169,0.2371698,0.001447379,0.007140853,0.7424098],"study_design_scores_gemma":[0.003997793,0.002570447,0.0006632943,0.0001522468,0.00003489758,0.0003126656,0.00260087,0.0989475,0.7222208,0.01715348,0.1508435,0.0005025081],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2083871,0.0003722988,0.7874762,0.00143838,0.0001791362,0.0006090237,0.0001775126,0.00001206382,0.001348342],"genre_scores_gemma":[0.9386696,0.00007917231,0.06015481,0.0003116846,0.000504699,0.00002881173,0.0001441274,0.00001388577,0.0000932503],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.7419073,"threshold_uncertainty_score":0.3008707,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03682672752606384,"score_gpt":0.3556736054863895,"score_spread":0.3188468779603256,"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."}}