Protein folding in the HP model on grid lattices with diagonals

Abstract

The protein folding problem, i.e., the computational prediction of the three-dimensional structure of a protein from its amino acid sequence, is one of the most important and challenging problems in computational biology. Since a complete simulation of the folding process of a protein is far too complex to handle, one tries to find an approximate solution by using a simplified, abstract model. One of the most popular models is the so-called HP model, where the hydrophobic interactions between the amino acids are considered to be the main force in the folding process, and furthermore the folding space is modeled by a two- or three-dimensional grid lattice. In this paper, we will present some approximation algorithms for the protein folding problem in the HP model on an extended grid lattice with plane diagonals. The choice of this kind of lattice removes one of the major drawbacks of the original HP model, namely the bipartiteness of the grid which severely restricts the set of possible foldings. Our algorithms achieve an approximation ratio of 26 15 ≈ 1.733 for the two-dimensional and of 8 5 = 1.6 for the three-dimensional lattice. This improves significantly over the best previously known approximation ratios for the protein folding problem in the HP model on any lattice.