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Table 1 Average execution time of TM-align, CPU-based ppsAlign, and ppsAlign with parameter settings (N iter = 3 and N seed = 20).

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

Dataset

Methods

RMSD100

Execution time (s)

Speedup of ppsAlign

D 1

ppsAlign

5.7

64

-

 

CPU-based ppsAlign

5.7

1596

24.9

 

TM-Align

5.7

2170

33.9

D 2

ppsAlign

5.3

41

-

 

CPU-based ppsAlign

5.3

899

21.9

 

TM-Align

5.3

1597

39.0

Total

ppsAlign

 

105

-

 

CPU-based ppsAlign

 

2495

23.8

 

TM-Align

 

3767

35.9

  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 other methods (CPU-based ppsAlign and TM-align) are 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 = 3 and N seed = 20