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Ligand Pose and Orientational Sampling in Molecular Docking

Figure 1

Orientational Matching Diagram.

A toy example illustrating the matching sphere orientational matching algorithm. A) Toy receptor with 4 matching spheres shown as circles and a toy ligand with 3 spheres shown as stars. B) The distance matrices constructed from these spheres are show in the upper right. C) The 2 possible orientational matches of the ligand spheres (as stars) onto the receptor spheres with a distance tolerance of 0.1 (assuming 3 matching nodes are used, in 3D this is usually 4). D) The additional two orientations produced when the distance tolerance is raised to 0.2.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0075992.g001