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 | |||
|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | 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) |
| Â | Â | 10 | 15 | -0.25 (0.269) | -0.11 (0.276) | 0.34 (0.261) | 0.31 (0.264) |
| Â | Â | 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) |
| Â | Â | 10 | 6 | 0.7 (0.357) | 0.73 (0.342) | -0.6 (0.400) | -0.33 0.472) |
| Â | Â | 20 | 13 | 0.72 (0.209) | 0.64 (0.232) | -0.47 (0.266) | -0.43 (0.272) |
1lng | 1lng/ 1z43 | 5 | 2 | - | - | - | - |
| Â | Â | 10 | 18 | 0.1 (0.249) | -0.15 (0.247) | 0.1 (0.249) | 0.14 (0.248) |
| Â | Â | 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) |
| Â | Â | 10 | 131 | -0.04 (0.088) | 0.02 (0.088) | 0.14 (0.087) | -0.03 (0.088) |
| Â | Â | 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) |
| Â | Â | 10 | 46 | 0.31 (0.143) | 0.39 (0.139) | 0.26 (0.146) | 0.2 (0.148) |
| Â | Â | 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) |
| Â | Â | 10 | 227 | 0.42 (0.061) | 0.34 (0.063) | 0.02 (0.067) | -0.4 (0.061) |
| Â | Â | 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) |
| Â | Â | 10 | 104 | 0.52 (0.085) | 0.49 (0.086) | -0.03 (0.099) | -0.32 (0.094) |
| Â | Â | 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) |
| Â | Â | 10 | 440 | 0.3 (0.046) | 0.21 (0.047) | 0.29 (0.046) | 0.13 (0.047) |
| Â | Â | 20 | 3290 | 0.41 (0.016) | 0.42 (0.016) | 0.04 (0.017) | 0.18 (0.017) |
| Â | Â | 5 | 28 | 0.32 | 0.26 | 0.21 | -0.01 |
Mean | 10 | 123.4 | 0.26 | 0.23 | 0.06 | -0.04 | |
| Â | Â | 20 | 962.6 | 0.37 | 0.34 | 0.01 | 0.13 |