Extended Data Fig. 9: Extended data corresponding to EternaFold development and test set evaluation.
From: RNA secondary structure packages evaluated and improved by high-throughput experiments
a) Comparing Vienna, CONTRAfold, and EternaFold predictions in predicting free energy of PUM binding. i) Replication of ddG_exp for both PUM WT and mutant binding from (Becker, 2019). The same calculation in Vienna 2 at 37 °C shows lower Root-mean-squared error (RMSE) (ii), but higher RMSE at 60 °C (iii). CONTRAfold 2 shows no improvement over Vienna at 37 °C (iv), but EternaFold shows modest improvement over both (v). b) Package performance for the S-Processed test set is qualitatively similar to results on the ArchiveII-NR test set (cf. Figure 3b). Error bars represent 95% confidence interval of the mean calculated with 1000 iterations of bootstrapping over n = 6 independent datasets, which contain 974 independent constructs total. c) Evaluating SHAPE- and DMS- directed folding. Error bars represent 95% confidence interval of the mean calculated with 1000 iterations of bootstrapping over n = 5 independent datasets of RNAs with known secondary structures,, which contain 47 constructs total. d) Potentials learned from EternaFold training and used in SHAPE-directed structure prediction.
