Table 4. The average accuracy of structure prediction with and without constraint with chemical modification data expressed as percentage of known canonical base pairs correctly predicted.

			Pseudoknot basepairs, %	Unconstrained		Constrained
RNA type	Ref(s).	Species		LFE	Best	LFE	Best
Signal recognition particle RNA	77, 81	Dog	0.0	18.2	97.7	84.1*	98.9*
5S rRNA in vivo	76	E. coli	0.0	26.3	86.8	86.8	97.4
Small subunit rRNA	25, 78	E. coli	1.6	39.0	49.0	63.3	73.2
RNase P	32, 80	Chromatium vinosum	10.5	53.5	81.6	53.5	81.6
RNase P	31, 80	Bacillus subtilis	7.1	56.3	70.5	56.3	68.8
RNase P	32, 80	E. coli	9.8	58.1†	73.4	64.5†	74.2
RNase P	30, 80	Saccharomyces cerevisiae	7.4	59.3	78.7	58.3	78.7
Telomerase RNA in vivo	43, 82,‡	Tetrahymena thermophila	10.5	65.8	84.2	65.8	84.2
group I bI5	78, 89	S. cerevisiae	5.0	78.2	83.2	81.5	83.2
group I Intron in vivo	43, 78	T. thermophila	4.7	83.0	90.7	83.0	90.7
group II Intron aI5c	27, 79	Yeast	0.0	86.1	89.1	77.7	82.2
group I Intron L-21 Sca I	37, 78	T. thermophila	5.0	86.7	90.0	89.2	90.8
5S rRNA in vivo	76	C. albicans	0.0	90.6†	90.6	90.6†	90.6
Large subunit rRNA (domain 1)	26, 78	E. coli	0.4	88.9	90.5	88.9	91.3
group II Intron	79, 90	Pylaiella littoralis	0.0	90.3†	94.6	90.3†	94.6
5S rRNA	24, 76	Mouse	0.0	94.4	100.0	88.9	94.4
Average				67.2	84.4	76.4	85.9

Accuracies are reported for both the lowest free energy structure (LFE) and best suboptimal structure in a set of up to 750 structures, generated with a window size of zero.

^*Results are reported for protein-bound RNA; when naked RNA chemical modification data are used, the accuracy is 64.8% for the lowest free energy structure and 89.8% for the best suboptimal structure.

^†Best of three or four structures having identical free energies.

^‡ten Dam, E., van Belkum, A. & Pleij, K. (1991) Nucleic Acids Res. 19, 6951.