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The analysis of the 3D structures of proteins is a very important problem in life sciences, since the geometric set-up of proteins has a deep relevance in many biological processes. The complexity of the analysis and the continuous increase in the number of proteins whose 3D structure is known, call for efficient and quick algorithms. Parallel processing is becoming an enabling tool for such research...
The retrieval and identification of geometrical motifs is an important open problem in bioinformatics. In previous works we presented Cross Motif Search (CMS), a novel algorithm which is able to search for recurring geometrical patterns in the secondary structure of proteins. A single run of CMS is able to look for similarities between a pair of proteins, and can be easily extended to compare each...
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