Table 3. Comparison of performance of distance-dependent energy, dihedral-dependent energy, and total energy of 3dRNAscore in test set II.

Decoy	RNA	Length	Method	Enrichment score (DI)
				Distance term	Dihedral term	Total
Position restrained dynamics and REMD (A)	1duq	26	X-ray	8.2	7.5	8.3
	1f27	30	X-ray	7.9	5.7	8.1
	1msy	27	X-ray	7.4	6.7	7.6
	1nuj	24	X-ray	7.3	7.5	7.4
	434d	14	X-ray	7.5	7.0	7.6
Normal modes (B)	1duq	26	X-ray	6.3	4.8	6.9
	1esy	19	NMR	6.5	5.2	6.5
	1f27	30	X-ray	6.7	4.3	6.7
	1i9v	76	X-ray	5.5	4.6	5.5
	1kka	17	NMR	6.9	2.6	6.9
	1msy	27	X-ray	6.3	4.7	6.7
	1nuj	24	X-ray	4.5	1.6	4.5
	1qwa	21	NMR	3.5	2.2	3.7
	1×9k	62	X-ray	3.1	2.5	3.1
	1xjr	46	X-ray	5.8	4.8	6.2
	1ykq	19	X-ray	5.2	5.0	5.0
	1zih	12	NMR	5.9	3.4	6.9
	28sp	28	NMR	6.1	5.4	5.7
	2f88	34	NMR	3.9	3.2	4.1
	434d	14	X-ray	6.5	5.2	6.9
FARNA (C)	1a4d	41	NMR	1.8	2.4	2.1
	1csl	28	X-ray	2.2	1.8	2.4
	1dqf	19	X-ray	3.6	2.0	3.6
	1esy	19	NMR	3.8	2.4	3.8
	1i9x	26	X-ray	4.2	1.6	4.0
	1j6s	24	X-ray	0.6	2.2	1.6
	1kd5	22	X-ray	2.4	1.6	2.4
	1kka	17	NMR	1.7	0.8	2.0
	1l2x	27	X-ray	0.4	1.4	1.5
	1mhk	32	X-ray	1.2	0.6	1.4
	1q9a	27	X-ray	3.0	1.6	3.2
	1qwa	21	NMR	1.2	0.6	1.4
	1xjr	46	X-ray	3.0	1.8	3.2
	1zih	12	NMR	6.8	2.4	6.8
	255d	24	X-ray	1.8	0.8	2.0
	283d	24	X-ray	1.7	0.6	1.8
	28sp	28	NMR	3.6	4.2	3.8
	2a43	26	X-ray	2.8	1.4	3.2
	2f88	34	NMR	3.5	2.1	3.6
Average values		(A)		7.66	6.88	7.80
		(B)		5.51	3.97	5.69
		(C)		2.59	1.70	2.83
		X-ray		4.43	3.43	4.65
		NMR		4.25	2.84	4.41
		All		4.37	3.24	4.57