Efficient algorithm improves prediction accuracy of RNA branching conformations, suggesting feasible exploration of alternative parameterizations.
Our results support the hypothesis that the conventional choice of multiloop parameters may limit prediction accuracy and that exploring alternative parameterizations is both tractable and worthwhile. The efficient partitioning algorithm we introduce makes this exploration feasible for longer sequences and larger datasets. Furthermore, we identify several open challenges in identifying the optimal structure.
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Poznanović et al. (2026) studied this question.
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