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Table 3 Comparison of the average and median RMSD and ComboT CT-opt values between different PDB ligand sets

From: PubChem3D: conformer ensemble accuracy

Accuracy measure 47,123 Ligands 157 Ligands 197 Ligands (Ref.[18])
  Before clustering After clustering Before clustering After clustering  
RMSD (Å) 0.39 (±0.24) / 0.30 0.57 (±0.36) / 0.50 0.40 (±0.26) / 0.33 0.65 (±0.31) / 0.61 0.67 / 0.51
ComboT CT-opt 1.77 (±0.20) / 1.85 1.61 (±0.27) / 1.70 1.75 (±0.22) / 1.83 1.55 (±0.25) / 1.58 1.56 / 1.64
  1. Numbers before and after slash are the mean and median, respectively, and numbers in parentheses are the standard deviations. The 47,123-ligand set are all the PDB ligand molecules considered in the present study, and the 157-ligand set contains 157 high-quality ligand molecules selected from the 47,123 compounds. The 197-ligand set contains 197 high-quality ligand molecules from the study by Hawkins et al. [18].