Figure 4: gRNAde compared to Rosetta for single-state design.

(a) We benchmark native sequence recovery of gRNAde, RDesign, Rosetta, FARNA and ViennaRNA on 14 RNA structures of interest identified by Das et al. (2010). gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45%) and all other methods. (b) Sequence recovery per sample for Rosetta and gRNAde, shaded by gRNAde’s perplexity for each sample. gRNAde’s perplexity is correlated with native sequence recovery for designed sequences (Pearson correlation: −0.76, Spearman correlation: −0.67). Full results on single-state test set are available in Appendix B and per-RNA results in Appendix Table 2.