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Table 2 Spearman correlation between the programs performance and the properties of the proteins or the ligands

From: Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds

  Glide Surflex Gold FlexX
A-best pose
 Properties of the proteins
  Crystal structure resolution NSC NSC NSC NSC
  Cavity sizea NSC NSC NSC NSC
  Hydrophobicityb NSC NSC NSC NSC
  Exposure NSC NSC NSC NSC
 Properties of the ligands
  MW 0.34 (6 × 10−4) NSC 0.33 (8 × 10−4) NSC
  AlogP NSC NSC NSC NSC
  PSA NSC NSC NSC NSC
  EC NSC NSC NSC NSC
  HBA NSC NSC NSC NSC
  HBD NSC NSC NSC NSC
  RC NSC NSC NSC NSC
  RB 0.47 (<10−4) 0.42 (<10−4) 0.50 (<10−4) NSC
B-top-rank
 Properties of the proteins
  Crystal structure resolution NSC NSC NSC NSC
  Cavity sizea NSC NSC NSC NSC
  Hydrophobicityb NSC NSC NSC NSC
  Exposure NSC NSC NSC NSC
 Properties of the ligands
  MW 0.34 (7 × 10−4) NSC NSC NSC
  AlogP NSC NSC NSC NSC
  PSA NSC NSC NSC NSC
  EC 0.34 (7 × 10−4) NSC NSC NSC
  HBA NSC NSC NSC NSC
  HBD NSC NSC NSC NSC
  RC NSC NSC NSC NSC
  RB 0.46 (<10−4) 0.35 (3 × 10−4) 0.48 (<10−4) NSC
  1. The correlations are calculated between the properties of the targets or the ligands and the RMSD of the best poses (A) obtained by docking with the 4 programs or the top-rank poses (B). The p-values are in parentheses. The correlations are considered non-significant for p-value ≥ 10−3, and therefore they are omitted
  2. NSC no significant correlation
  3. aCavity size = total number of the cavity heavy atoms at 4 Å from the surface
  4. bHydrophobicity of the cavity = fraction of carbon atoms (FCA) among the cavity heavy atoms