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Table 3 Average CPU time* required to calculate one structure alignment of ten different algorithms

From: MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments

Algorithm MALIDUP-sq MALIDUP-ns MALISAM-sq MALISAM-ns
DaliLite 0.910s 1.019s 0.445s 0.539s
TM-align 0.111s 0.087s 0.055s 0.043s
CE 0.152s 0.055s
MICAN 0.134s 0.134s 0.098s 0.097s
DEDAL 5.734s 6.000s 0.272s 0.259s
SNAP 1.517s 1.743s 0.962s 1.128s
GANGSTA+ 0.270s 0.273s 0.185s 0.190s
SCALI 8.272s 8.153s 2.723s 2.870s
MASS 0.138s 0.136s 0.105s 0.106s
SAMO 0.454s 0.455s 0.166s 0.163s
  1. *CPU times are measured on a PC with Intel Core-i7 2.93 GHz processor.