Abstract

In this paper, we study the protein threading problem, which was proposed for finding a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard by Lathrop, we study polynomial time approximation algorithms. First we show that the protein threading problem is MAX SNP-hard. Next we show that the protein threading problem can be approximated within a factor 4 for a special case in which a graph representing interaction between residues (amino acids) is planar. This case corresponds to a fi-sheet substructure, which appears in most protein structures. 1 Introduction The protein folding problem is, given an amino acid sequence (a string), to find its correctly folded 3D protein structure. It is one of the most important computational problems in molecular biology. Although this problem can be defined as a minimization problem, it is too hard to be solved directly. Recently, an indirect approach called inverse folding was proposed [2, 4,...

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