Accelerating large-scale protein structure alignments with graphics processing units
1 Informatics Institute, University of Missouri, Columbia, MO, USA
2 Department of Electrical and Computer Engineering, University of, Columbia, MO, USA
3 Department of Computer Science, University of Missouri, Columbia, 65211, MO, USA
BMC Research Notes 2012, 5:116 doi:10.1186/1756-0500-5-116Published: 22 February 2012
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
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 allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.