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Table 3 Average execution time of MAMMOTH and ppsAlign with parameter settings (N iter = 1 and N seed = 8).

From: Accelerating large-scale protein structure alignments with graphics processing units

Dataset

Methods

RMSD100

Execution time (s)

Speedup of ppsAlign

D 1

ppsAlign

6.3

10

-

 

MAMMOTH

10.3

470

47.0

D 2

ppsAlign

5.9

8

-

 

MAMMOTH

9.2

255

31.9

Total

ppsAlign

 

18

-

 

MAMMOTH

 

725

40.3

  1. RMSD100 is the expected value of cRMSD if the two protein structures were 100 residues long. ppsAlign is running on NVIDIA Tesla C2050 GPU card and MAMMOTH is running on a computer with AMD Opetron dual-core 1000 series processor at 1.8 GHz and 8 GB RAM. The parameter settings of ppsAlign are N iter = 1 and N seed = 8
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BMC Research Notes

ISSN: 1756-0500

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