Skip to main content

Table 3 Results of scoring the decoys in the GRAMM-generated unbound docking set

From: DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

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
  1. Correlation coefficients were calculated for scatter plots from Figure 6.