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Accurate prediction of RNA secondary structure remains a cornerstone of functional genomics, drug design, and synthetic biology. We present FPRE080, a novel computational pipeline that couples a refined thermodynamic model with a fast stochastic sampling algorithm to locate the minimal free‑energy (MFE) conformation of medium‑length RNAs (50‑300 nt). Using a curated benchmark (Dataset 015958) comprising 1 200 experimentally validated structures, FPRE080 achieves a mean sensitivity of 86 % and positive predictive value of 84 %, surpassing state‑of‑the‑art tools (RNAfold, CONTRAfold, and LinearFold) while requiring only 30 % of the runtime. The method is freely available under an open‑source license and can be integrated into existing pipelines for high‑throughput RNA analysis.
| Variant | Sensitivity | Precision | Runtime (ms) | |--------------------------|------------|-----------|--------------| | Full Turner (no pruning) | 0.84 | 0.82 | 210 | | TPP‑38 only (DP) | 0.85 | 0.83 | 140 | | SBS (B = 4) only | 0.80 | 0.78 | 95 | | Full FPRE080 | 0.86 | 0.84 | 78 |
Both pruning and stochastic beam search contribute synergistically; removing either component degrades either speed or accuracy.