Table 2:

Full results for Figure 4 comparing gRNAde to Rosetta, FARNA and ViennaRNA for single-state design on 14 RNA structures of interest identified by Das et al. [2010]. Rosetta and FARNA recovery values are taken from Das et al. [2010], Supplementary Table 2.

PDB ID	Description	ViennaRNA Recovery	FARNA Recovery	Rosetta Recovery	gRNAde (single-state)
					Recovery	Perplexity	2D self-cons.
1CSL	RRE high affinity site	0.25	0.20	0.44	0.5719	1.2812	0.8644
1ET4	Vitamin B12 binding RNA aptamer	0.25	0.34	0.44	0.6250	1.3457	−0.0135
1F27	Biotin-binding RNA pseudoknot	0.30	0.36	0.37	0.3437	1.6203	0.4523
1L2X	Viral RNA pseudoknot	0.24	0.45	0.48	0.4721	1.3181	0.5692
1LNT	RNA internal loop of SRP	0.33	0.27	0.53	0.5843	1.4337	0.1379
1Q9A	Sarcin/ricin domain from E.coli 23S rRNA	0.27	0.40	0.41	0.5044	1.3411	0.0597
4FE5	Guanine riboswitch aptamer	0.29	0.28	0.36	0.5300	1.3824	0.9116
1X9C	All-RNA hairpin ribozyme	0.26	0.31	0.50	0.5000	1.3905	0.6630
1XPE	HIV-1 B RNA dimerization initiation site	0.27	0.24	0.40	0.7037	1.2177	0.7768
2GCS	Pre-cleavage state of glmS ribozyme	0.25	0.26	0.44	0.5078	1.3053	0.4062
2GDI	Thiamine pyrophosphate-specific riboswitch	0.25	0.38	0.48	0.6500	1.2363	−0.0251
2OEU	Junctionless hairpin ribozyme	0.23	0.30	0.37	0.9519	1.0913	0.7768
2R8S	Tetrahymena ribozyme P4-P6 domain	0.27	0.36	0.53	0.5689	1.1881	0.7281
354D	Loop E from E. coli 5S rRNA	0.28	0.35	0.55	0.4410	1.4938	0.0430
	Overall recovery:	0.27	0.32	0.45	0.5682