Table 3.

Results of scoring the decoys in the GRAMM-generated unbound docking set

Complex PDB code	Protein/ RNA PDB codes	RMSD threshold (decoy vs native)	Number of decoys below threshold (per 10,000)	Correlation coefficient
				DARS-RNP potential (std. error)	QUASI-RNP potential (std. error)	Varani potential (std. error)	Fernandez potential (std. error)
2rkj	1y42/ 1y0q	5	4	-0.58 (0.576)	0.17 (0.697)	-0.6 (0.566)	1 (0.000)
		10	15	-0.25 (0.269)	-0.11 (0.276)	0.34 (0.261)	0.31 (0.264)
		20	87	0.09 (0.108)	0.21 (0.106)	0.06 (0.108)	0.51 (0.093)
2r8s	2r8s/ 1hr2	5	3	1 (0.000)	1 (0.000)	-1 (0.000)	-1 (0.000)
		10	6	0.7 (0.357)	0.73 (0.342)	-0.6 (0.400)	-0.33 0.472)
		20	13	0.72 (0.209)	0.64 (0.232)	-0.47 (0.266)	-0.43 (0.272)
1lng	1lng/ 1z43	5	2	-	-	-	-
		10	18	0.1 (0.249)	-0.15 (0.247)	0.1 (0.249)	0.14 (0.248)
		20	48	0.73 (0.101)	0.71 (0.104)	0.4 (0.135)	0.53 (0.125)
2pxv	2pxv/ 1cql	5	14	0.69 (0.209)	0.02 (0.289)	0.28 (0.277)	-0.19 (0.283)
		10	131	-0.04 (0.088)	0.02 (0.088)	0.14 (0.087)	-0.03 (0.088)
		20	948	-0.08 (0.032)	-0.02 (0.033)	0.13 (0.032)	0.17 (0.032)
1e7k	2jnb/ 1e7k	5	7	-0.08 (0.446)	0.09 (0.445)	0.6 (0.358)	0.11 (0.444)
		10	46	0.31 (0.143)	0.39 (0.139)	0.26 (0.146)	0.2 (0.148)
		20	938	0.19 (0.032)	0.17 (0.032)	0.14 (0.032)	0.17 (0.032)
1wpu	1wpv/ 1wpu	5	125	0.63 (0.070)	0.67 (0.067)	-0.08 (0.090)	-0.3 (0.086)
		10	227	0.42 (0.061)	0.34 (0.063)	0.02 (0.067)	-0.4 (0.061)
		20	1165	0.5 (0.025)	0.37 (0.027)	0.02 (0.029)	-0.21(0.029)
3bso	1sh0/ 3bso	5	34	0.48 (0.155)	0.32 (0.167)	-0.1 (0.176)	-0.09 (0.176)
		10	104	0.52 (0.085)	0.49 (0.086)	-0.03 (0.099)	-0.32 (0.094)
		20	1212	0.42 (0.026)	0.41 (0.026)	-0.21 (0.028)	0.09 (0.029)
2jea	2je6/ 2jea	5	35	0.16 (0.172)	0.22 (0.170)	0.34 (0.164)	0.44 (0.156)
		10	440	0.3 (0.046)	0.21 (0.047)	0.29 (0.046)	0.13 (0.047)
		20	3290	0.41 (0.016)	0.42 (0.016)	0.04 (0.017)	0.18 (0.017)
		5	28	0.32	0.26	0.21	-0.01
Mean		10	123.4	0.26	0.23	0.06	-0.04
		20	962.6	0.37	0.34	0.01	0.13

Correlation coefficients were calculated for scatter plots from Figure 6.