Table 3. P-values obtained in a Wilcoxon signed-rank test comparing the distribution of S(1), S(3), and S(5) values of AnnapuRNA and other docking programs.

Docking was performed using native conformation of a ligand as an input. Two-tailed p-values ≤ 0.05 are in bold. Data referenced in the main text are underlined.

		Wilcoxon signed-rank test p-value (two tailed)
		docking program: rdock (dock_solv)			docking program: rdock (dock)			docking program: AutoDock Vina			docking program: iDock
AnnapuRNA variant	Compared method	S(1)	S(3)	S(5)	S(1)	S(3)	S(5)	S(1)	S(3)	S(5)	S(1)	S(3)	S(5)
AnnapuRNA DL (2013)	LigandRNA (2013)	0.201	0.601	0.296	0.104	0.095	0.198	0.933	0.939	0.444	0.719	0.964	0.863
	LigandRNA (updated)	0.162	0.455	0.286	0.211	0.088	0.122	1.000	0.977	0.390	0.478	0.964	0.713
	rDock (dock)	0.009	0.042	0.036	0.032	0.024	0.044	0.381	0.019	0.206	0.009	< 0.001	0.001
	rDock (dock_solv)	0.005	0.057	0.056	0.016	0.014	0.027	0.171	0.035	0.087	0.125	0.128	0.027
	RF-Score-VS v2	0.001	0.001	0.002	< 0.001	0.001	0.002	0.173	0.117	0.206	0.365	0.094	0.016
AnnapuRNA DL (2016)	LigandRNA (2013)	0.465	0.811	0.078	0.819	0.429	0.140	0.540	0.484	0.848	0.339	0.755	0.636
	LigandRNA (updated)	0.313	0.984	0.073	0.475	0.394	0.085	0.597	0.513	0.768	0.194	0.755	0.567
	rDock (dock)	0.023	0.136	0.008	0.889	0.053	0.008	0.799	0.069	0.033	0.050	< 0.001	0.002
	rDock (dock_solv)	0.014	0.368	0.022	0.647	0.062	0.009	0.407	0.079	0.011	0.241	0.078	0.025
	RF-Score-VS v2	0.001	0.006	0.001	0.011	0.001	0.002	0.033	0.264	0.762	0.130	0.049	0.047
AnnapuRNA kNN (2013)	LigandRNA (2013)	0.053	0.542	0.636	0.200	0.465	0.082	0.459	0.867	0.809	0.468	0.442	0.316
	LigandRNA (updated)	0.033	0.469	0.619	0.456	0.404	0.048	0.346	0.886	0.809	0.264	0.442	0.183
	rDock (dock)	0.004	0.039	0.050	0.361	0.068	0.009	0.107	0.028	0.135	0.052	< 0.001	< 0.001
	rDock (dock_solv)	0.002	0.086	0.121	0.264	0.072	0.008	0.038	0.039	0.061	0.144	0.017	0.001
	RF-Score-VS v2	< 0.001	0.001	0.005	0.003	0.001	0.001	0.373	0.245	0.334	0.166	0.217	0.472
AnnapuRNA kNN (2016)	LigandRNA (2013)	0.130	0.538	0.363	0.118	0.330	0.217	0.952	0.808	0.438	0.145	0.666	0.690
	LigandRNA (updated)	0.104	0.433	0.349	0.266	0.297	0.131	0.980	0.808	0.386	0.068	0.666	0.556
	rDock (dock)	0.011	0.079	0.044	0.127	0.182	0.024	0.260	0.021	0.327	0.108	0.001	0.001
	rDock (dock_solv)	0.007	0.136	0.079	0.097	0.072	0.028	0.170	0.028	0.199	0.260	0.050	0.024
	RF-Score-VS v2	0.001	0.001	0.004	0.001	0.003	0.002	0.098	0.309	0.119	0.042	0.153	0.059