Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures

Abstract. Protein structure analysis is one of the most important research issues in the post-genomic era, and faster and more accurate query data structures for such 3-D structures are highly desired for research on proteins. This paper proposes a new data structure for indexing protein 3-D structures. For strings, there are many efficient indexing structures such as suffix trees, but it has been considered very difficult to design such sophisticated data structures against 3-D structures like proteins. Our index structure is based on the suffix trees and is called the geometric suffix tree. By using the geometric suffix tree for a set of protein structures, we can search for all of their substructures whose RMSDs (root mean square deviations) or URMSDs (unit-vector root mean square deviations) to a given query 3-D structure are not larger than a given bound. Though there are O(N2 ) substructures, our data structure requires only O(N) space where N is the sum of lengths of the set of ...

• Type: Conference
• Year: 2006
• Where: CPM
• Authors: Tetsuo Shibuya
• Keywords: 3-d Structure, Combinatorics, CPM 2006, Data Structure, Suffix Tree