Table 2 Results of scoring the decoys in the GRAMM-generated 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 10,000) | Correlation coefficient | |||
|---|---|---|---|---|---|---|
| Â | Â | Â | DARS-RNP potential (std. error) | QUASI-RNP potential (std. error) | Varani potential (std. error) | Fernandez potential (std. error) |
1urn | 5 | 21 | 0.38 (0.212) | 0.25 (0.222) | 0.45 (0.205) | -0.15 (0.227) |
| Â | 10 | 72 | 0.51 (0.103) | 0.41 (0.109) | 0.46 (0.106) | -0.01 (0.120) |
| Â | 20 | 352 | 0.6 (0.043) | 0.45 (0.048) | 0.29 (0.051) | -0.42 (0.049) |
1ec6 | 5 | 87 | 0.3 (0.103) | 0.28 (0.104) | 0.4 (0.099) | -0.12 (0.108) |
| Â | 10 | 155 | 0.7 (0.058) | 0.68 (0.059) | 0.53 (0.069) | 0.03 (0.081) |
| Â | 20 | 1079 | 0.65 (0.023) | 0.56 (0.025) | 0.31 (0.029) | 0.18 (0.030) |
1fxl | 5 | 81 | 0.62 (0.088) | 0.64 (0.086) | 0.62 (0.088) | 0.46 (0.100) |
| Â | 10 | 143 | 0.81 (0.049) | 0.82 (0.048) | 0.61 (0.067) | 0.62 (0.066) |
| Â | 20 | 1732 | 0.61 (0.019) | 0.52 (0.021) | 0.3 (0.023) | 0.29 (0.023) |
1cvj | 5 | 38 | 0.62 (0.131) | 0.49 (0.145) | 0.55 (0.139) | 0.34 (0.157) |
| Â | 10 | 76 | 0.95 (0.036) | 0.91 (0.048) | 0.48 (0.102) | 0.72 (0.081) |
| Â | 20 | 1638 | 0.49 (0.022) | 0.43 (0.022) | 0.18 (0.024) | 0.5 (0.021) |
1jid | 5 | 16 | 0.13 (0.265) | 0.18 (0.263) | 0.73 (0.183) | 0.54 (0.225) |
| Â | 10 | 29 | 0.13 (0.191) | 0.09 (0.192) | 0.59 (0.155) | 0.28 (0.185) |
| Â | 20 | 175 | -0.06 (0.076) | 0.04 (0.076) | 0.58 (0.062) | 0.2 (0.074) |
Mean | 5 | 49 | 0.41 | 0.37 | 0.55 | 0.22 |
| Â | 10 | 95 | 0.62 | 0.58 | 0.54 | 0.33 |
| Â | 20 | 995 | 0.46 | 0.4 | 0.33 | 0.15 |