Finding compact structural motifs

Abstract

Protein structural motif detection has important applications in structural genomics. Compared with sequence motifs, structural motifs are more sensitive in revealing 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 due to employing exhaustive search strategies. This paper studies a reasonably restricted version of this problem: the compact structural motif problem. We prove that this restricted version is still NP-hard, and we present a polynomial-time approximation scheme to solve it. This is the first approximation algorithm with a guaranteed ratio for the protein structural motif problem. 11A preliminary version of this paper appeared in CPM'2007. © 2009 Elsevier B.V. All rights reserved.