Protein Folding in the Hexagonal Prism Lattice with Diagonals (1407.4650v1)

Abstract: Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence. Secondary structure refers to local sub-structures of protein. Mostly founded secondary structures are alpha helix and beta sheets. Since, it is a problem of great potential complexity many simplified energy model have been proposed in literature on basis of interaction of amino acid residue in protein. Here we use well researched Hydrophobic-Polar (HP) energy model. In this paper, we proposed hexagonal prism lattice with diagonal that can overcome the problems of other lattice structure, e.g., parity problem. We give two approximation algorithm for protein folding on this lattice. Our first algorithm leads us to similar structure of helix structure which is commonly found in protein structure. This motivated us to find next algorithm which improves the algorithm ratio of 9/7.