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Table 4 Pearson correlation coefficients and root mean squared error between experimental binding affinity and binding affinity predicted by DLIGAND, DLIGAND2, and X-Score using docking poses generated by eight docking programs along with the results from the docking programs

From: DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

Docking program Pearson correlation coefficient Root mean squared error
Self DLIGAND DLIGAND2 X-Score Self DLIGAND DLIGAND2 X-Score
AutoDock 0.404 0.465 0.537 0.547 1.91 1.77 1.69 1.68
AutoDock Vina 0.501 0.459 0.519 0.536 1.74 1.78 1.72 1.69
rDock 0.102 0.463 0.535 0.507 2.01 1.78 1.70 1.76
LeDock 0.426 0.457 0.532 0.54 1.82 1.78 1.69 1.69
UCSF DOCK 0.195 0.427 0.498 0.488 1.97 1.81 1.74 1.76
iDock 0.485 0.461 0.522 0.54 1.75 1.78 1.71 1.69
GalaxyDock 0.487 0.464 0.537 0.532 1.75 1.78 1.69 1.71
iGEMDOCK 0.384 0.444 0.501 0.502 1.85 1.80 1.76 1.82
Average 0.373 0.455 0.523 0.524 1.85 1.79 1.71 1.73