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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

OAI identifier:
oai:arXiv.org:1103.1264

Provided by:
arXiv.org e-Print Archive

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