Table 1.

Prediction results for RNA structures with 3 or more strands

Name	Ref.	Strands	Residues	NanoFolderJK	NanoFolder	Pairs	Time (s)
hairpin riboz. (2P7F)	42	4	60	0.82	0.82	0.56	0.053
nanosquare (3P59)	2	4	100	0.40	0.36	0.08	0.052
antiprism (lower half)	5	4	504	0.74	0.75	0.69	0.617
antiprism (upper half)	5	4	504	0.78	0.73	0.62	0.654
RNA-square	1	4	368	0.97	0.97	0.36	0.425
hexameric ring	7	6	264	0.33	0.63	0.10	0.199
antiprism	5	8	1008	0.78	0.78	0.63	2.913
6-stranded cube	3	6	288	1.00	1.00	0.53	0.233
10-stranded cube	3	10	332	0.94	0.94	0.57	0.252

Strands: number of input RNA sequences; Ref.: literature reference; Residues: total number of nucleotides; NanoFolerJK: NanoFolder results (Matthews correlation coefficient MCC) using Jack-knifing (such that current structure was not used during training); pairs results (MCC) from the NUPACK pairs program; NanoFolder: results (MCC) of NanoFolder using standard parameters. Time: run-time of the NanoFolder program (in seconds), evaluated using a Linux PC with a 3.0 GHz Intel Xeon processor.