Least-Squares Fitting of Two 3-D Point Sets
IEEE Transactions on Pattern Analysis and Machine Intelligence
Finding similar regions in many strings
STOC '99 Proceedings of the thirty-first annual ACM symposium on Theory of computing
Finding the consensus shape for a protein family
Proceedings of the eighteenth annual symposium on Computational geometry
Multiple Structural Alignment and Core Detection by Geometric Hashing
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Hard problems in similarity searching
Discrete Applied Mathematics - Discrete mathematics & data mining (DM & DM)
A parameterized algorithm for protein structure alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance
FAW '08 Proceedings of the 2nd annual international workshop on Frontiers in Algorithmics
Clustering 100,000 Protein Structure Decoys in Minutes
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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 polynomialtime 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.