Table 1.

Summary table of the accuracy of the 2D structure prediction programs on the test set of DNA aptamers

CentroidFold	RNAfold	Mfold	PDB_ID	Structure	Len
1.	1.	1.	1JVE	Triplex-DNA	27
1.	1.	1.	1NGU	Hairpin with pseudoknots	27
1.	1.	1.	2OEY	Hairpin with loops	25
1.	1.	1.	2VWJ	Hairpin with dangling ends	26
1.	1.	1.	3THW	Hairpin with loops	53
1.	1.	1.	4HT4	Hairpin with dangling ends	28
0.92	1.	1.	1NGO	Hairpin	27
0.92	1.	1.	5N2Q	Hairpin with dangling ends	26
0.77	1.	1.	3H25	Hairpin with dangling ends	27
0.55	1.	1.	1AW4	Hairpin with pseudoknots	27
1.	0.96	1.	6CCE	Hairpin with dangling ends	57
0.6	0.6	1.	1B4Y	Triplex-DNA	30
0.91	0.95	0.95	2N8A	Double hairpin	45
0.75	0.65	0.95	3HXQ	Two-forked with pseudoknots	41
0.88	0.88	0.94	5HRT	Hairpin with loops	34
0.93	1.	0.93	1GN7	Triplex-DNA	32
0.93	1.	0.93	1WAN	Triplex-DNA	32
0.8	1.	0.93	2ARG	Hairpin with pseudoknots	30
0.93	0.93	0.93	4F41	Hairpin	32
0.93	0.93	0.93	4F43	Hairpin	32
0.93	0.93	0.93	4TMU	Hairpin with dangling ends	29
0.87	0.93	0.93	4ER8	Hairpin with dangling ends	32
0.75	0.75	0.93	5HRU	Hairpin with loops and pseudoknots	32
0.84	0.92	0.92	134D	Triplex-DNA	25
0.84	0.92	0.92	135D	Triplex-DNA	25
0.84	0.92	0.92	136D	Triplex-DNA	25
0.9	0.9	0.9	5D2Q	Hairpin	40
0.89	0.89	0.89	4CEI	Hairpin with dangling ends	37
0.83	0.89	0.89	4CEH	Hairpin with dangling ends	37
0.88	0.92	0.88	5LD2	Hairpin with dangling ends	51
0.83	0.88	0.88	3U44	Hairpin with dangling ends	36
0.61	0.66	0.88	1SNJ	Two forked	36
0.5	0.66	0.88	1EZN	Two forked	36
0.85	0.85	0.85	3U4Q	Hairpin with dangling ends	27
0.61	0.73	0.85	2F1Q	Three-forked	42
0.8	0.7	0.85	4REC	Double-stranded	40
0.92	0.84	0.84	1OMH	Hairpin with dangling ends	25
0.92	0.84	0.84	1QX0	Hairpin with dangling ends	25
0.92	0.84	0.84	1S6M	Hairpin with dangling ends	25
0.92	0.84	0.84	1ZM5	Hairpin with dangling ends	25
0.76	0.84	0.84	5D23	Hairpin	26
0.83	0.88	0.83	5D2S	Hairpin	36
0.33	0.73	0.73	2M91	Hairpin with G-quadruplex	30
0.8	0.45	0.72	3HXO	Two forked with pseudoknots	40
0.62	0.7	0.7	2M8Z	Hairpin with G-quadruplex	27
0.77	0.68	0.67	4CEJ	Hairpin with dangling ends	46
0.65	1.	0.63	5CMX	Double-stranded with G-quadruplex	30
0.62	0.87	0.62	2M90	Hairpin with G-quadruplex	32
0.14	0.2	0.61	2M92	Hairpin with G-quadruplex	34
0.5	0.56	0.56	2M93	Hairpin with G-quadruplex	32
0.48	0.48	0.51	4I7Y	Double-stranded with G-quadruplex	27
0.53	1.	0.46	2HY9	G-quadruplex	26
0.53	1.	0.46	2JPZ	G-quadruplex	26
0.53	1.	0.46	2LPW	G-quadruplex	26
0.53	1.	0.46	5MVB	G-quadruplex	26
0.53	1.	0.46	6CCW	G-quadruplex	26
0.52	1.	0.44	2JSL	G-quadruplex	25
0.52	1.	0.44	2JSQ	G-quadruplex	25
0.48	0.92	0.4	2MBJ	G-quadruplex	27
0.48	0.64	0.4	2M53	G-quadruplex	25
0.46	0.92	0.38	5Z80	G-quadruplex	26
0.58	0.38	0.38	5MTA	G-quadruplex	34
0.58	0.38	0.38	5MTG	G-quadruplex	34
0.42	0.71	0.35	2MS9	G-quadruplex	28
0.42	0.71	0.35	4U5M	G-quadruplex	28
0.42	0.71	0.32	2N3M	G-quadruplex	28
0.1	1.	0.25	201D	G-quadruplex	28
0.36	1.	0.24	5J6U	G-quadruplex	25
0.1	1.	0.14	230D	G-quadruplex	28