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◇ bioRxiv2026-09-17· bioinformatics

FORGE audits residue-level information encoded in RNA tertiary structure geometry

L. Gow, J. Li, X. Tan, K. Liang, N. Gui, B. Luo

原始摘要(英文原文)· Original 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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FORGE audits residue-level information encoded in RNA tertiary structure geometry — 科研速览 Science Skim