A 2O(n1-(1/d)log n) Time Algorithm for d-Dimensional Protein Folding in the HP-Model
نویسندگان
چکیده
The protein folding problem in the HP-model is NP-hard in both 2D and 3D [4, 6]. The problem is to put a sequence, consisting of two characters H and P, on a d-dimensional grid to have the maximal number of HH contacts. We design a 2 1− 1 d log n) time algorithm for ddimensional protein folding in the HP-model. In particular, our algorithm has O(2 √ n log ) and O(2 2 3 log ) computational time in 2D and 3D respectively. The algorithm is derived via our separator theorem for points on a d-dimensional grid. For example, for a set of n points P on a 2-dimensional grid, there is a separator with at most 1.129 √ n points that partitions P into two sides with at most ( 2 3 )n points on each side. Our separator theorem for grid points has a greatly reduced upper bound than that for the general planar graph [2].
منابع مشابه
Geometric Separators and Their Applications to Protein Folding in the HP-Model
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