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

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

	Glide	Surflex	Gold	FlexX
A-best pose
Properties of the proteins
Crystal structure resolution	NSC	NSC	NSC	NSC
Cavity size^a	NSC	NSC	NSC	NSC
Hydrophobicity^b	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 size^a	NSC	NSC	NSC	NSC
Hydrophobicity^b	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

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
NSC no significant correlation
^aCavity size = total number of the cavity heavy atoms at 4 Å from the surface
^bHydrophobicity of the cavity = fraction of carbon atoms (FCA) among the cavity heavy atoms

ISSN: 1758-2946