Differentiable RNA Secondary Structure Extraction for Deep Learning

Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret because current benchmarks may overestimate generalization across RNA families. We present the Comprehensive Hierarchical Annotation of Non-coding RNA Groups (CHANRG), a benchmark of 170{,}083 structurally non-redundant RNAs curated from more than 10 million sequences in Rfam~15.0 using structure-aware deduplication, genome-aware split design and multiscale structural evaluation. Across 29 predictors, foundation-model methods achieved the highest held-out accuracy but lost most of that advantage out of distribution, whereas structured decoders and direct neural predictors remained markedly more robust. This gap persisted after controlling for sequence length and reflected both loss of structural coverage and incorrect higher-order wiring. Together, CHANRG and a padding-free, symmetry-aware evaluation stack provide a stricter and batch-invariant framework for developing RNA structure predictors with demonstrable out-of-distribution robustness.

The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the structural flexibility of RNA, as, unlike proteins, RNA molecules exist as dynamic conformational ensembles. Thus, committing to a single predicted structure discards information relevant to binding. Here, we show that this obstacle can be addressed by extracting pre-structural embeddings, which are intermediate representations from a biomolecular foundation model captured before the structure decoding step. Pre-structural embeddings implicitly encode conformational ensemble information without requiring predicted structures. We build ZeroFold, a transformer-based model that combines pre-structural embeddings from Boltz-2 for both protein and RNA molecules through a cross-modal attention mechanism to predict binding affinity directly from sequence. To support training and evaluation, we construct PRADB, a curated dataset of 2,621 unique protein-RNA pairs with experimentally measured affinities drawn from four complementary databases. On a held-out test set constructed with 40% sequence identity thresholds, ZeroFold achieves a Spearman correlation of 0.65, a value approaching the ceiling imposed by experimental measurement noise. Under progressively fairer evaluation conditions that control for training-set overlap, ZeroFold compares favourably with respect to leading structure-based and leading sequence-based predictors, with the performance gap widening as sequence similarity to competitor training data is reduced. These results illustrate how pre-structural embeddings offer a representation strategy for flexible biomolecules, opening a route to affinity prediction for protein-RNA pairs for which no structural data exist.

Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce RiboSphere, a framework that learns discrete geometric representations of RNA by combining vector quantization with flow matching. Our design is motivated by the modular organization of RNA architecture: complex folds are composed from recurring structural motifs. RiboSphere uses a geometric transformer encoder trained using mean-centered coordinates and random rotation augmentation to produce geometry-aware features, which are discretized with finite scalar quantization (FSQ) into a finite vocabulary of latent codes. Conditioned on these discrete codes, a flow-matching decoder reconstructs atomic coordinates, enabling high-fidelity structure generation. We find that the learned code indices are enriched for specific RNA motifs, suggesting that the model captures motif-level compositional structure rather than acting as a purely compressive bottleneck. Across benchmarks, RiboSphere achieves strong performance in structure reconstruction (RMSD 1.25,Å, TM-score 0.84), and its pretrained discrete representations transfer effectively to inverse folding and RNA--ligand binding prediction, with robust generalization in data-scarce regimes. Code is available at https://github.com/Zhangz312/RiboSphere.