Finding compact structural motifs

Abstract

Protein structure motif detection is one of the fundamental problems in Structural Bioinformatics. Compared with sequence motifs, structural motifs are more sensitive in detecting the evolutionary relationships among proteins. A variety of algorithms have been proposed to attack this problem. However, they are either heuristic without theoretical performance guarantee, or inefficient for employing an exhaustive search strategy. Here, we study a reasonably restricted version of this problem: the compact structural motif problem. In this paper, we prove that this restricted version is still NP-hard, and we present a polynomial-time approximation scheme to solve it. To the best of our knowledge, this is the first approximation algorithm with a guarantee ratio for the protein structural motif problem. © Springer-Verlag Berlin Heidelberg 2007.