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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
    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)
  10 72 0.51 (0.103) 0.41 (0.109) 0.46 (0.106) -0.01 (0.120)
  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)
  10 155 0.7 (0.058) 0.68 (0.059) 0.53 (0.069) 0.03 (0.081)
  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)
  10 143 0.81 (0.049) 0.82 (0.048) 0.61 (0.067) 0.62 (0.066)
  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)
  10 76 0.95 (0.036) 0.91 (0.048) 0.48 (0.102) 0.72 (0.081)
  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)
  10 29 0.13 (0.191) 0.09 (0.192) 0.59 (0.155) 0.28 (0.185)
  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
  10 95 0.62 0.58 0.54 0.33
  20 995 0.46 0.4 0.33 0.15
  1. Correlation coefficients were calculated for scatter plots from Figure 5.