Finding compact structural motifs

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. 1 1 A preliminary version of this paper appeared in CPM’2007.

Authors

• Dongbo Bu
• Ming Li
• Shuai Cheng Li
• Jianbo Qian
• Jinbo Xu

Keywords

• Compact Structural motif
• NP-Hardness
• Approximation algorithm