On the protein folding problem in 2D-triangular lattices

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 1-2log n/n-1 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. © 2013 Islam and Rahman; licensee BioMed Central Ltd.