Publication at Faculty of Mathematics and Physics |
2013
Abstract
Similarity measures for the protein structures are quite complex and require significant computational time. We propose a parallel approach to this problem to fully exploit the computational power of current CPU architectures.
This paper summarizes experience and insights acquired from the parallel implementation of the SProt similarity method, its database access method, and also the wellknown TM-score algorithm. The implementation scales almost inearly with the number of CPUs and achieves 21.4x speedup on a 24-core system.
The implementation is currently employed in the web application http://siret.cz/p3s.