Abstract
In this paper, we present a novel approximation algorithm to solve the protein folding problem in HP model. Our algorithm is polynomial in terms of the length of the given HP string. The expected approximation ratio of our algorithm is for n ≥ 6, where n2 is the total number of H’s in a given HP string. The expected approximation ratio tends to reach 1 for large values of n. Hence our algorithm is expected to perform very well for larger HP strings.
Highlights
A long standing problem in Molecular Biology and Biochemistry is to determine the three dimensional structure of a protein given only the sequence of amino acid residues that compose protein chains
The HP model is based on the assumption that hydrophobicity is the dominant force in protein folding
We present an approximation algorithm for protein folding in 2D-triangular lattice
Summary
A long standing problem in Molecular Biology and Biochemistry is to determine the three dimensional structure of a protein given only the sequence of amino acid residues that compose protein chains. The length of the hexagon (or lattice) is the total number of points along the D-sides. Note carefully that if we can fully fill a hexagon with z lattice points with a single H-run and get a total of k edges, the number of total bonds will be k − z + 1. We show this by considering a hexagon and adjusting its depth keeping the total number of points fixed Suppose that the total number of points is z and the depth of the hexagon x and length. If we fail to fill up all the points of a regular hexagon we put the rest of the H-runs outside the hexagon in a single row (see Figure 13) and compute the total number of bonds.
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