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Table 2 Comparison of the scoring powers of BsN-Score, BgN-Score, SNN-Score, Random Forests (RF), and 16 conventional SFs on the core test set Cr

From: BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes

Scoring function N 1 R p 2 R s 3 SD 4 RMSEtest5 RMSEtrain6
BsN-Score::XARG 195 0.816 0.799 1.38 1.386 1.366
BgN-Score::XARG 195 0.804 0.798 1.42 1.449 1.403
RF::XARG 195 0.801 0.790 1.43 1.498 1.442
SNN-Score::X 195 0.675 0.685 1.76 1.760 1.704
X-Score::HMScore 195 0.644 0.705 1.83 1.865 1.730
DrugScoreCSD 195 0.569 0.627 1.96 - -
SYBYL::ChemScore 195 0.555 0.585 1.98 - -
DS::PLP1 195 0.545 0.588 2.00 - -
GOLD::ASP 195 0.534 0.577 2.02 - -
SYBYL::G-Score 195 0.492 0.536 2.08 - -
DS::LUDI3 195 0.487 0.478 2.09 - -
DS::LigScore2 193 0.464 0.507 2.12 - -
GlidScore-XP 178 0.457 0.435 2.14 - -
DS::PMF 193 0.445 0.448 2.14 - -
GOLD::ChemScore 178 0.441 0.452 2.15 - -
SYBYL::D-Score 195 0.392 0.447 2.19 - -
DS::Jain 189 0.316 0.346 2.24 - -
GOLD::GoldScore 169 0.295 0.322 2.29 - -
SYBYL::PMF-Score 190 0.268 0.273 2.29 - -
SYBYL::F-Score 185 0.216 0.243 2.35 - -
  1. 1 Number of complexes in Cr with positive (favorable) binding scores using this SF [14].
  2. 2 R p is the Pearson correlation coefficient between predicted and measured BA values of complexes in Cr.
  3. 3 R s is the Spearman correlation coefficient between predicted and measured BA values of complexes in Cr.
  4. 4 SD is the standard deviation of errors between predicted and measured BA values of complexes in Cr based on Equation 3 in [15].
  5. 5 RMSE is the root-mean-square of errors between predicted and measured BA values of the test complexes in Cr. Test RMSE is not available for conventional SFs except for X-Score::HMScore that we have re-constructed.
  6. 6 RMSE is the root-mean-square of errors between predicted and measured BA values of out-of-sample complexes in the training set Pr. Training RMSE is not available for conventional SFs except for X-Score::HMScore that we have re-constructed.