Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology
M-tree: An Efficient Access Method for Similarity Search in Metric Spaces
VLDB '97 Proceedings of the 23rd International Conference on Very Large Data Bases
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
3D zernike descriptors for content based shape retrieval
SM '03 Proceedings of the eighth ACM symposium on Solid modeling and applications
An Efficient Index-based Protein Structure Database Searching Method
DASFAA '03 Proceedings of the Eighth International Conference on Database Systems for Advanced Applications
Evaluating Top-k Queries over Web-Accessible Databases
ICDE '02 Proceedings of the 18th International Conference on Data Engineering
iDistance: An adaptive B+-tree based indexing method for nearest neighbor search
ACM Transactions on Database Systems (TODS)
A multi-resolution surface distance model for k-NN query processing
The VLDB Journal — The International Journal on Very Large Data Bases
Bioinformatics
High-dimensional indexing with oriented cluster representation for multimedia databases
ICME'09 Proceedings of the 2009 IEEE international conference on Multimedia and Expo
Exact indexing for support vector machines
Proceedings of the 2011 ACM SIGMOD International Conference on Management of data
DTMBIO 2012: international workshop on data and text mining in biomedical informatics
Proceedings of the 21st ACM international conference on Information and knowledge management
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This paper exploits efficient indexing techniques for protein structure search where protein structures are represented as vectors by 3D-Zernike Descriptor (3DZD). 3DZD compactly represents a surface shape of protein tertiary structure as a vector, and the simplified representation accelerates the structural search. However, further speed up is needed to address the scenarios where multiple users access the database simultaneously. We address this need for further speed up in protein structural search by exploiting two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. The results show that both iDistance and iKernel significantly enhance the searching speed. In addition, we introduce an extended approach for protein structure search based on indexing techniques that use the 3DZD characteristic. In the extended approach, index structure is constructured using only the first few of the numbers in the 3DZDs. To find the top-k similar structures, first top-10 x k similar structures are selected using the reduced index structure, then top-k structures are selected using similarity measure of full 3DZDs of the selected structures. Using the indexing techniques, the searching time reduced 69.6% using iDistance, 77% using iKernel, 77.4% using extended iDistance, and 87.9% using extended iKernel method.