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

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 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 http://siret.cz/p3s.

BibTeX:

@inproceedings{galgonek_parallelization_2013,
    title = {{On the Parallelization of the SProt Measure and the TM-Score Algorithm}},
    author = {Galgonek, Jakub and Kruliš, Martin and Hoksza, David},
    year = {2013},
    booktitle = {{Euro-Par 2012: Parallel Processing Workshops}},
    editor = {Caragiannis, Ioannis and Alexander, Michael and Badia, Rosa Maria and Cannataro, Mario and Costan, Alexandru and Danelutto, Marco and Desprez, Frédéric and Krammer, Bettina and Sahuquillo, Julio and Scott, Stephen L. and Weidendorfer, Josef},
    publisher = {Springer},
    series = {{Lecture Notes in Computer Science}},
    location = {Berlin, Heidelberg},
    doi = {10.1007/978-3-642-36949-0_27},
    isbn = {978-3-642-36949-0},
    pages = {238--247},
}

Proceedings paper