RNA structural characterization of RNA-binding protein binding sites
Bibliographic record
Abstract
The interaction between RNA and RNA-binding proteins (RBPs) facilitates key processes, such as gene expression regulation, mRNA transport, and splicing, within the lifetime of the RNA.Studies of these interactions have demonstrated the importance of not only RNA sequencelevel motifs but also of the RNA structural context surrounding the RBP binding site.Whereas sequence-focused studies have identified well-characterized sequence elements serving as RBP binding sites, the structural considerations remain limited to a small set of RNA secondary structural elements.We present a study identifying local 3D RNA modules associated with the binding of specific RBPs.Using datasets composed of 3D RNA modules extracted from experimentally-determined structures, we annotate eukaryotic mRNA sequences and relate the presence of these local structures with RBP binding.We report several specific RNA modules, each associated with the binding of specific RBPs, along with a link between certain modules and mRNA subcellular localization.i List of Tables 3.1 z-Score statistic and associated counts for each RBP-module pair . . . . . . . .33 3.2 Validation counts . . . . . . . . . . .
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".