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.
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Qian, J., Li, S.C., Bu, D., Li, M., Xu, J. (2007). Finding Compact Structural Motifs. In: Ma, B., Zhang, K. (eds) Combinatorial Pattern Matching. CPM 2007. Lecture Notes in Computer Science, vol 4580. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73437-6_16
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DOI: https://doi.org/10.1007/978-3-540-73437-6_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73436-9
Online ISBN: 978-3-540-73437-6
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