Table I.

Assessment of the statistical significance of the correlation of radius of gyration, total number of contacts, and the scoring function presented in this work with RMSD and sensitivity. The p-value of the t-distribution for the null hypothesis is reported. For radius of gyration and total number of contacts, a single linear regression to either sensitivity or RMSD was performed. For the scoring function, a separate regression was performed to either sensitivity or RMSD. The null hypothesis was that the slope for a given independent variable was not different from zero and this was tested using a one-tailed t-test on the slope and the standard error of the slope. Large radii of gyration and a large number of contacts correlate with at least one of a low RMSD and a large sensitivity with significance (p < 0.05) for all molecules. The scoring function correlates with both RMSD and sensitivity for all molecules with the exception of the RMSD of the HCV IRES RNA

	SRP Alu Domain	HCV IRES	Hammerhead ribozyme	Yeast tRNAPhe	Group I P4-P6 Domain	P4-P6 with MOHCA
p-value. of Rg for RMSD	0.004	0.13	0.02	8×10−6	2×10−6	0.002
p-value of Rg for sensitivity	0.06	0.005	0.18	0.007	0.05	0.29
p-value of total contacts for RMSD	0.14	0.47	0.03	0.19	0.45	0.02
p-value of total contacts for sensitivity	2×10−5	0.008	0.03	0.0001	6×10−5	2×10−5
p-value of score for RMSD	0.03	0.24	0.004	0.0001	0.0006	0.0007
p-value of score for sensitivity	0.002	0.0004	0.02	6×10−6	6×10−5	0.004