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Polynomial cases of the Discretizable Molecular Distance Geometry Problem

By Leo Liberti, Carlile Lavor, Benoit Masson and Antonio Mucherino


An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between corresponding point pairs. When the graph represents the backbone of a protein, one can exploit the natural vertex order to show that the search space for feasible embeddings is discrete. The corresponding decision problem can be solved using a binary tree based search procedure which is exponential in the worst case. We discuss assumptions that bound the search tree width to a polynomial size

Topics: Computer Science - Computational Geometry, Computer Science - Computational Engineering, Finance, and Science, Computer Science - Data Structures and Algorithms, Quantitative Biology - Quantitative Methods
Year: 2011
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