{"id":"W4409325490","doi":"10.1261/rna.080267.124","title":"SMDesigner: a program to design sequence mutations to assess RNA structure","year":2025,"lang":"en","type":"article","venue":"RNA","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Armand Frappier Museum; Institut National de la Recherche Scientifique","funders":"","keywords":"Biology; RNA; Nucleic acid structure; Computational biology; Genetics; Nucleic acid secondary structure; Sequence (biology); Mutation; Pseudoknot; Function (biology); Non-coding RNA; Riboswitch; Indel; Sequence analysis; 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":[0.0001446453,0.0001403611,0.0001173337,0.00006940242,0.0001024463,0.00005960579,0.0002812896,0.000125824,0.00003488564],"category_scores_gemma":[0.0001743427,0.0001312994,0.00004979811,0.0002465463,0.00001824509,0.000003104627,0.00007634818,0.00004224044,0.00002628135],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002077707,"about_ca_system_score_gemma":0.0001483386,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000109439,"about_ca_topic_score_gemma":0.000009916218,"domain_scores_codex":[0.9990804,0.00009320096,0.0001420343,0.0003418756,0.0001070127,0.0002354856],"domain_scores_gemma":[0.9993883,0.00001739279,0.00003128593,0.0003521035,0.00009060039,0.0001203293],"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":[0.0000373166,0.0000223664,0.00001507567,0.00001091972,0.00002608888,0.000003117844,0.00002947649,0.0003634286,0.896009,0.0004189804,0.00172153,0.1013426],"study_design_scores_gemma":[0.00008381045,0.0002749207,0.0001244685,0.00003316404,0.00001711124,0.000003220617,0.00002161125,0.00003625837,0.9778284,0.001733353,0.01968537,0.0001582791],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2542656,0.000215332,0.7393633,0.001966385,0.0003061849,0.001822984,0.00004406708,0.00007920718,0.00193699],"genre_scores_gemma":[0.8850137,0.000008199306,0.1114922,0.001103746,0.00007352976,0.00028559,0.00002456832,0.00001625481,0.001982241],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.6307481,"threshold_uncertainty_score":0.5354235,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04036766083868758,"score_gpt":0.3267754109573578,"score_spread":0.2864077501186702,"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."}}