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

  • Jakub Galgonek
  • Martin Kruliš
  • David Hoksza
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7640)


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 21.4× speedup on a 24-core system. The implementation is currently employed in the web application


protein structure similarity parallel optimization 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Jakub Galgonek
    • 1
  • Martin Kruliš
    • 1
  • David Hoksza
    • 1
  1. 1.Departement of Software EngineeringCharles University in PraguePraha 1Czech Republic

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