Least-Squares Fitting of Two 3-D Point Sets
IEEE Transactions on Pattern Analysis and Machine Intelligence
International Journal of Robotics Research
Matrix computations (3rd ed.)
Estimating 3-D rigid body transformations: a comparison of four major algorithms
Machine Vision and Applications - Special issue on performance evaluation
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Introduction to algorithms
Optimal suffix tree construction with large alphabets
FOCS '97 Proceedings of the 38th Annual Symposium on Foundations of Computer Science
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Geometric suffix tree: a new index structure for protein 3-d structures
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Searching Protein 3-D Structures in Linear Time
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
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Protein structure analysis is one of the most important research issues in the post-genomic era, and faster and more accurate index data structures for such 3-D structures are highly desired for research on proteins. The geometric suffix tree is a very sophisticated index structure that enables fast and accurate search on protein 3-D structures. By using it, we can search from 3-D structure databases for all the substructures whose RMSDs (root mean square deviations) to a given query 3-D structure are not larger than a given bound. In this paper, we propose a new data structure based on the geometric suffix tree whose query performance is much better than the original geometric suffix tree. We call the modified data structure the prefix-shuffled geometric suffix tree (or PSGST for short). According to our experiments, the PSGST outperforms the geometric suffix tree in most cases. The PSGST shows its best performance when the database does not have many substructures similar to the query. The query is sometimes 100 times faster than the original geometric suffix trees in such cases.