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
On approximation algorithms for local multiple alignment
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
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
A parameterized algorithm for protein structure alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
| Hi-index | 5.23 |
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.