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bioRxiv · 10.64898/2026.07.05.736550

FORGE reveals an information spectrum encoded in RNA tertiary-structure geometry

Gow, L.·Li, J.·Tan, X.·Li, L.
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Abstract

Coarse RNA coordinate representations are widely used, yet the biological information they encode remains unquantified. We introduce FORGE, which converts a seven-atom RNA geometry representation into 935 interpretable descriptors and reports which residue-level annotations this geometry supports. On 4,135 post-2025 RNA chains, FORGE recovered 64.6% of native nucleotides; a six-atom control lacking the glycosidic nitrogen retained 58.5%, locating most of this signal in phosphate-sugar geometry. Confidence was sharply graded: abstaining from the least-confident half of positions raised accuracy to 94.4%, yet many chains remained only partially identifiable. The same descriptors predicted base-pair state far better than a DMS-like proxy or protein-proximal context. Native-decoy, OpenKnot and solved-pseudoknot analyses showed that nucleotide identifiability, foldability and experimental design score are separable: AlphaFold3 reproduced the experimental fold for one of four AI-designed constructs and none of the sequences FORGE read from their geometry. FORGE provides a reproducible audit layer for RNA structural interpretation.

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Gow, L., Li, J., Tan, X., Li, L.. 2026-07-06. FORGE reveals an information spectrum encoded in RNA tertiary-structure geometry. https://doi.org/10.64898/2026.07.05.736550

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