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. 2012 Apr 20;7(4):e35457. doi: 10.1371/journal.pone.0035457

Figure 2. Evaluation of molecular docking using high resolution crystal structure complexes.

Figure 2

A. Comparison of top ranked pose obtained from molecular docking (yellow) with the crystallographic binding mode (blue) of the Kdoα(2→4)Kdoα(2-OAll):S25-39 complex (PDB 3OKK). B. Comparison of top ranked pose (yellow) obtained from molecular docking with the crystallographic binding mode (blue) of the Kdoα(2→8)Kdoα(2→4)Kdoα(2-OAll):S73-2 complex (PDB 3HZV). C. Schematic representation of interactions in the Kdoα(2→4)Kdoα(2-OAll):S25-39 predicted by molecular docking. D. Schematic representation of interactions in the Kdoα(2→8)Kdoα(2→4)Kdoα(2-OAll):S73-2 complex. Molecular docking carried out using GOLD 4.1.1. Figures 2A and 2B prepared using PyMOL [64]. Figures 2C and 2D prepared using LIGPLOT [65]. Legend to Figures 2C and 2D: hydrogen bonds – green dashes; hydrophobic interactions – red arcs; carbon – black; oxygen – red; nitrogen – blue; ligand bonds – purple; protein bonds – orange.