Approximate Protein Folding in Oz through Frequency Analysis

The protein folding problem consists in determining the spatial shape of a protein once the linear sequence of its amino acids is known. Its solution uses mathematical models of the protein, the HP model being one of the simplest. Despite its simplicity, the problem of protein folding inside the HP model is still NP-complete. In this paper we rephrase the HP model in a way that allows us to devise a new heuristic to burst the performance of automatic protein folding inside the HP model. Our implementation of protein folding in Mozart/Oz shows that our heuristic is very eective in practice and features a high level of precision for the solution it computes