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Table 5 Analysis of the reasons for the 9 targets ranking failure

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

Target RMSD (Å) of the best best-pose RMSD (Å) of the best top-rank pose Reasons for incorrect ranking Due to the scoring functions? Possible recommendations
cp3a4 2.03 Surflex 4.14 Glidescore Coordination bond No  
xiap 1.25 Surflex 3.78 FlexX Ligand not well anchored in the binding site No  
hdac8 0.91 Glidescore 2.91 Goldscore The metal ion chelation is not considered explicitly or not well parametrized Yes With modified parameters of the metal, the top-rank pose is correct
hs90a 0.32 Gold 9.54 Glidescore, FlexX, Goldscore An off-center pose is privileged No Possibility of the existence of a secondary site difficult to reach (dynamical considerations)
igf1r 0.72 Surflex 2.32 Surflex Difference in protonation No Include in situ protonation in the docking procedure
cxcr4 1.94 Gold 2.95 Surflex Difference in protonation No Similar to igf1r
pnph 0.65 Gold 3.14 Glidescore Difference in protonation No Similar to igf1r
hivpr 1.97 Surflex 2.26 Glidescore, Goldscore The difference is located in a loose or exposed to solvent part of the ligand No The difference is not a problem
tysy 1.27 Surflex 2.7 Goldscore The difference is located in a loose or exposed to solvent part of the ligand No Similar to hivpr
  1. For each ligand, all poses of the pool were ranked by each program and we only consider the top-rank pose with the smallest RMSD, without any consideration of the program