Molecular Docking Algorithm Based on Shape Complementarity Principles
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PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.

Short Overview:

PatchDock algorithm is inspired by object recognition and image segmentation techniques used in Computer Vision. Docking can be compared to assembling a jigsaw puzzle. When solving the puzzle we try to match two pieces by picking one piece and searching for the complementary one. We concentrate on the patterns that are unique for the puzzle element and look for the matching patterns in the rest of the pieces. PatchDock employs a similar technique. Given two molecules, their surfaces are divided into patches according to the surface shape. These patches correspond to patterns that visually distinguish between puzzle pieces. Once the patches are identified, they can be superimposed using shape matching algorithms. The algorithm has three major stages:

Surface Segmentation


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