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Table 2 Average execution time of Fr-TM-align and ppsAlign with parameter settings (N iter = 6 and N seed = 30).

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

Dataset

Methods

RMSD100

Execution time (s)

Speedup of ppsAlign

D 1

ppsAlign

5.4

326

-

 

Fr-TM-align

5.4

19849

60.9

D 2

ppsAlign

5.1

224

-

 

Fr-TM-align

5.1

15729

70.2

Total

ppsAlign

 

550

-

 

Fr-TM-align

 

35578

64.7

  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 Fr-TM-align 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 = 6 and N seed = 30
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BMC Research Notes

ISSN: 1756-0500

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