PSIST (protein structures using suffix trees) uses suffix trees to index protein 3D structure. It first converts the 3D structure into a structure-feature sequence over a new structural alphabet, which is then used to index protein structures. The PSIST index makes it very fast to query for a matching structural fragment.
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Feng Gao and Mohammed J. Zaki,
PSIST: A Scalable Approach to Indexing Protein Structures using Suffix Trees.
Journal of Parallel and Distributed Computing, 68(1):55-63. Jan 2008