Parallel Processing Method of Protein Surface Motifs Extraction

Y. Shimizu, N.L. Shrestha, and T. Ohkawa (Japan)


bioinformatics, surface motifs, parallel processing, vector pairs, protein, active sites.


We have proposed a method of extracting surface mo tifs: SUrface MOtif mining MOdule (SUMOMO). Sur face motifs can be defined as commonly appearing patterns of shape and physical properties in protein molecular sur faces. Surface motif extraction takes a huge amount of time and memory space from much input protein. In this paper, a method of reducing the required memory and calculation time is proposed by parallel processing of SUMOMO. Af ter applying this method, processing time was shortened by 33%, and the amount of memory used was reduced to 20% using five worker nodes.

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