Accelerating large-scale protein structure alignments with graphics processing units.

BMC Research Notes
Bin PangChi-Ren Shyu

Abstract

Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper a...Continue Reading

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Citations

Feb 1, 2014·Journal of Molecular Modeling·Dariusz MrozekBożena Małysiak-Mrozek
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Bin PangChi-Ren Shyu
Mar 15, 2015·IEEE Transactions on Nanobioscience·Wei P FeinsteinMichal Brylinski
Jul 13, 2016·Briefings in Bioinformatics·Marco S NobileDaniela Besozzi
Nov 26, 2015·BioMed Research International·Anuj Sharma, Elias S Manolakos

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Software Mentioned

NCBI
ppsAlign
JAVA
SA Tableau Search
DALI
SIMT
align
BLAST
Basic Local Alignment Search Tool
CUDA

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