Supplementary Figure 3: Stereo diagrams comparing the results of the various docking protocols for GPP2.
From: More-powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules
The side chain of Ile113 is not shown, to reveal the hydrogen bond, drawn as dotted lines, between the main chain nitrogen of this residue and the ligand oxygen. Residues from VP1 are shown in blue and Ile24 from VP3 in orange. (a) Overlay of the docked ligand GPP2 (light green) by QMPLD method and the structurally determined conformation of GPP2 (magenta) (RMSD for all inhibitor atoms 1.3 Å). (b) Overlay of the docked ligand GPP2 by GOLD (violet) and the structurally determined conformation of GPP2 (magenta) (RMSD for all inhibitor atoms 0.9 Å). (c) Overlay of the docked ligand GPP2 by Rosetta (gray) and the structurally determined conformation of GPP2 (magenta) (note GPP2 is docked upside down).
