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. Author manuscript; available in PMC: 2022 Oct 1.
Published in final edited form as: Nat Protoc. 2021 Sep 24;16(10):4799–4832. doi: 10.1038/s41596-021-00597-z

Fig. 7 ∣. Matching and dielectric boundary spheres drive changes to sampling and scoring in DOCK3.7.

Fig. 7 ∣

a, the crystal ligand is shown as orange sticks in the receptor pocket (gray). Matching spheres derived from the coordinates of the crystal ligand are shown in yellow and remain fixed during sphere perturbation. Random spheres (blue) are calculated with the program SphGen, and a set of spheres are selected that are near the crystal ligand. In a matching sphere scan, only the random spheres are perturbed and a new set is obtained (green). b, the crystal ligand (orange) is again shown in the context of the receptor binding pocket (gray). Dielectric boundary spheres (cyan) cover the binding surface around the crystal ligand to alter the electrostatic or desolvation potentials at the boundary between solvent and protein.