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2018 | OriginalPaper | Buchkapitel

10. Massively Parallel Searching of 3D Protein Structure Similarities on CUDA-Enabled GPU Devices

verfasst von : Dariusz Mrozek

Erschienen in: Scalable Big Data Analytics for Protein Bioinformatics

Verlag: Springer International Publishing

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Abstract

Finding common molecular substructures in complex 3D protein structures is still challenging. This is especially visible when scanning entire databases containing tens or even hundreds of thousands protein structures. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) promise to give a high speedup of many time-consuming and computationally demanding processes over their original implementations on CPUs. In this chapter, we will see that massive parallelization of the 3D structure similarity searching on many core CUDA-enabled GPU devices leads to reduction of the execution time of the process and allows to perform it in real time.

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Titel: Massively Parallel Searching of 3D Protein Structure Similarities on CUDA-Enabled GPU Devices
verfasst von: Dariusz Mrozek
Verlag: Springer International Publishing
Buch: Scalable Big Data Analytics for Protein Bioinformatics
Print ISBN: 978-3-319-98838-2

Electronic ISBN: 978-3-319-98839-9

Copyright-Jahr: 2018
DOI: https://doi.org/10.1007/978-3-319-98839-9_10

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