title: Accelerating large-scale protein structure alignments with graphics processing units.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Informatics Institute, University of Missouri, Columbia, MO, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Pang
authors.forename: Nan
authors.initials: N
authors.lastname: Zhao
authors.forename: Michela
authors.initials: M
authors.lastname: Becchi
authors.forename: Dmitry
authors.initials: D
authors.lastname: Korkin
authors.forename: Chi-Ren
authors.initials: CR
authors.lastname: Shyu
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins