Skip to main content

Table 2 Performance of six pairwise structure alignment tools on benchmarks MALIDUP and MALISAM

From: MADOKA: an ultra-fast approach for large-scale protein structure similarity searching

BenchmarkMethodNaliRMSDTM-scoreTotal Time (s)
MALIDUPDeepAlign 85.52.610.62210.2
 DALI 83.52.650.600115.3
 MATT 82.32.470.60863.0
 Formatt 70.62.190.54285.1
 TM-align 87.02.620.6316.4
 MADOKA91.73.430.6311.2
MALISAMDeepAlign 61.32.960.5214.3
 DALI 61.03.110.51547.4
 MATT 56.22.740.48616.2
 Formatt 44.92.420.41133.1
 TM-align 61.13.060.5172.9
 MADOKA62.82.720.5550.7
  1. *These are detailed in [33]