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.
Bu, D., Li, M., Li, S. C., Qian, J., & Xu, J. (2009). Finding compact structural motifs. Theoretical Computer Science, 410(30–32), 2834–2839. https://doi.org/10.1016/j.tcs.2009.03.023