On the Parallelization of the SProt Measure and the TM-Score Algorithm

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 linearly 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.