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We introduce the concept of multi-directional width-bounded geometric separators and obtain an improved separator for grid graphs. This yields an improved exact algorithm for the protein folding problem in the HP-model. For a grid graph G with n grid points P, there exists a separator A ⊆ P such that A has at most points, and G − A has two disconnected subgraphs each with at most nodes. This improves the previous upper bound of . We also derive a lower bound for such a separator in grid graphs.