{"id":"W1969668230","doi":"10.1371/journal.pcbi.1000823","title":"Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures","year":2010,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Uppsala Universitet; Albert-Ludwigs-Universität Freiburg","keywords":"RNA; Computational biology; Nucleic acid structure; Folding (DSP implementation); Sequence (biology); Biology; Computer science; Biological system; Algorithm; Bioinformatics; Gene; Genetics","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":[0.0002822506,0.0001469446,0.0001807352,0.00004953469,0.0001984694,0.00001414323,0.0001553925,0.0001621283,0.00002993731],"category_scores_gemma":[0.0001858944,0.0001062742,0.00008197719,0.00004880703,0.0001567431,0.000004427303,0.00003547693,0.0001212528,2.141952e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003415049,"about_ca_system_score_gemma":0.00005416319,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002705928,"about_ca_topic_score_gemma":0.00004998581,"domain_scores_codex":[0.9990367,0.0001648438,0.000244543,0.0003064623,0.00009015114,0.0001572561],"domain_scores_gemma":[0.9989988,0.0005158348,0.0001616293,0.0001089068,0.0001755704,0.00003926761],"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":[0.0002169175,0.00001360812,0.0001445996,0.00002414235,0.0001817408,1.59918e-7,0.0001202839,0.001149825,0.9812726,0.009690876,0.0000115164,0.007173663],"study_design_scores_gemma":[0.0007196029,0.0002470364,0.002173075,0.000006174062,0.00004587511,0.00003014237,0.00006885534,0.008089082,0.9166822,0.07131962,0.0004707365,0.0001475202],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7130301,0.0001478509,0.2859391,0.0002888772,0.0001762571,0.0002747811,0.0001099995,0.000007342117,0.00002569624],"genre_scores_gemma":[0.9279934,0.000009030005,0.07134989,0.000239341,0.0002112032,0.0000451984,0.0001316118,0.00001342598,0.000006952862],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2149633,"threshold_uncertainty_score":0.4333735,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03700790182889908,"score_gpt":0.3010013837854018,"score_spread":0.2639934819565027,"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."}}