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. Author manuscript; available in PMC: 2018 Feb 1.
Published in final edited form as: Nat Protoc. 2017 Jan 12;12(2):255–278. doi: 10.1038/nprot.2016.169

FIGURE 10.

FIGURE 10

Best models from docking the signal transducing protein HPr (PDB ID 1POH) to the glucose-specific phosphocarrier protein E2A (PDB ID 1F3G) without and with restraints. The receptor protein, E2A, is shown as grey surface. A. Ligand position at the center of the second largest cluster (shown as cyan cartoon) from docking without restraints. The position is slightly shifted relative to the native ligand binding position, shown as magenta cartoon. B. Ligand position at the center of the largest cluster (shown as blue cartoon) from docking with restraints. The ligand is now turned a few degrees around an axis perpendicular to the center of the receptor.