On the approximation of protein threading

AbstractIn this paper, we study the protein threading problem, which was proposed for predicting a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard, we study polynomial time approximation algorithms. We show several hardness results for the approximation, which includes a MAX SNP-hardness result. We also show approximation algorithms for a special case and a general case, where a graph representing interactions between amino acid residues is restricted to be planar in a special case. For this special case, we obtain a constant approximation ratio