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This could be achieved by pre-computing the indexes of proteins and
arranging them in a hash table. Then, queries are evaluated based on a voting scheme using the hash table. This
voting scheme replaces the seed generation process.
In this lecture, we look into the voting scheme used in 3dSEARCH [2]. The algorithm is based on the concept of
geometric hashing [1] developed in the eld of computer vision. The basic idea is to represent all secondary structure
elements (SSEs) from all target proteins with a large, highly redundant hash (or index) table. Once the table has been
constructed, every SSE from a given query structure can be compared simultaneously to the entire set of SSEs of the
target structures, by indexing the SSE into the table...
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