Approximation Algorithms for Three Dimensional Protein Folding

Abstract

Predicting protein secondary structures using lattice models is one of the most studied computational problems in bioinformatics. Here the secondary structure or three dimensional structure of a protein is predicted from its amino acid sequence. The secondary structure refers to local sub-structures of a protein. Mostly founded secondary structures are alpha helix and beta sheets. Simplified energy models have been proposed in the literature on the basis of interaction of amino acid residues in proteins. Here we use well researched Hydrophobic-Polar (HP) energy model. In this paper, we propose the hexagonal prism lattice with diagonals that can overcome the problems of other lattice structures, e.g., parity problem. We give two approximation algorithms for protein folding on this lattice. Our first algorithm leads us to a similar structure of helix structure that is commonly found in a protein structure. This motivates us to propose the next algorithm with a better approximation ratio.