Table 1 Results of scoring the decoys in the Varani bound docking set
From: DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
Complex PDB code | RMSD threshold (decoy vs native) | Number of decoys below threshold (per 2,000) | Correlation coefficient | |||
|---|---|---|---|---|---|---|
| Â | Â | Â | DARSI-RNP potential (std. error) | QUASI-RNP potential (std. error) | Varani potential (std. error) | Fernandez potential (std. error) |
1urn | 5 | 726 | 0.77 (0.024) | 0.7 (0.027) | 0.37 (0.035) | -0.56 (0.031) |
| Â | 10 | 1457 | 0.83 (0.015) | 0.79 (0.016) | 0.27 (0.025) | -0.24 (0.025) |
| Â | 20 | 1967 | 0.81 (0.013) | 0.79 (0.014) | 0.21 (0.022) | -0.1 (0.022) |
1ec6 | 5 | 907 | 0.81 (0.019) | 0.79 (0.020) | 0.57 (0.027) | -0.08 (0.033) |
| Â | 10 | 1446 | 0.9 (0.011) | 0.89 (0.012) | 0.38 (0.024) | -0.05 (0.026) |
| Â | 20 | 1979 | 0.87 (0.011) | 0.86 (0.011) | 0.31 (0.021) | -0.02 (0.022) |
1fxl | 5 | 881 | 0.94 (0.012) | 0.95 (0.011) | 0.87 (0.017) | 0.61 (0.027) |
| Â | 10 | 1366 | 0.96 (0.008) | 0.96 (0.008) | 0.82 (0.015) | 0.74 (0.018) |
| Â | 20 | 1758 | 0.93 (0.009) | 0.94 (0.008) | 0.7 (0.017) | 0.83 (0.013) |
1cvj | 5 | 936 | 0.96 (0.009) | 0.96 (0.009) | 0.5 (0.028) | 0.85 (0.017) |
| Â | 10 | 1217 | 0.97 (0.007) | 0.97 (0.007) | 0.61 (0.023) | 0.92 (0.011) |
| Â | 20 | 1947 | 0.93 (0.008) | 0.93 (0.008) | 0.46 (0.020) | 0.9 (0.010) |
1jid | 5 | 828 | 0.58 (0.028) | 0.58 (0.028) | 0.35 (0.033) | 0.33 (0.033) |
| Â | 10 | 1485 | 0.72 (0.018) | 0.71 (0.018) | 0.3 (0.025) | 0.39 (0.024) |
| Â | 20 | 1978 | 0.7 (0.016) | 0.69 (0.016) | 0.27 (0.022) | 0.29 (0.022) |
Mean | 5 | 855.6 | 0.81 | 0.8 | 0.53 | 0.23 |
| Â | 10 | 1394.2 | 0.88 | 0.87 | 0.47 | 0.35 |
| Â | 20 | 1925.8 | 0.85 | 0.84 | 0.39 | 0.38 |