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High-Performance Computational Solutions in Protein BioinformaticsParallel CUDA-Based Protein 3D Structure Similarity Searching

High-Performance Computational Solutions in Protein Bioinformatics: Parallel CUDA-Based Protein... [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 a 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.] http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png

High-Performance Computational Solutions in Protein BioinformaticsParallel CUDA-Based Protein 3D Structure Similarity Searching

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Publisher
Springer International Publishing
Copyright
© The Author(s) 2014
ISBN
978-3-319-06970-8
Pages
49 –79
DOI
10.1007/978-3-319-06971-5_3
Publisher site
See Chapter on Publisher Site

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 a 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.]

Published: Jun 5, 2014

Keywords: Proteins; 3D protein structure; Tertiary structure; Similarity searching; Structure matching; Structure comparison; Structure alignment; Parallel computing; GPU; CUDA

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