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Table 1 Comparisons of structure alignment algorithms with rms distance and the number of aligned atoms m.

From: Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

  Protein Pairs SAMO Dali CE Lund
   rms m λ rms m rms m rms m
Reductases 1DHF a - 8DFR 0.7 182 6.0 0.7 182 0.7 182 0.7 182
  1DHF a - 4DFR a 1.8 156 6.0 2.0 154 2.0 154 2.0 156
  1DHF a - 3DFR 1.6 159 6.0 1.7 158 1.7 158 1.7 159
  8DFR - 4DFR a 1.9 157 6.0 2.0 155 2.0 155 2.0 157
  8DFR - 3DFR 1.6 159 6.0 1.8 159 1.8 158 1.8 160
  4DFR a - 3DFR 1.5 156 6.0 1.5 154 1.5 155 1.5 155
Globins 2HHB a - 2HHB b 1.4 139 6.0 1.4 138 1.5 139 1.4 139
  2HHB a - 1MBD 1.5 141 6.0 1.5 139 1.6 141 1.5 141
  2HHB a - 2HBG 1.6 140 6.0 1.7 138 1.7 136 1.6 138
  2HHB a - 1ECD 2.2 131 6.0 2.3 129 2.6 128 2.3 130
  1MBD - 2HBG 2.0 141 8.0 2.2 140 2.1 140 2.0 140
  2HHB b - 1MBD 1.6 145 6.0 1.6 145 1.6 144 1.6 145
  2HHB b - 2HBG 1.7 137 6.0 2.0 135 1.9 134 1.7 136
  2HHB b - 1MBA 2.2 140 6.0 2.3 138 2.4 139 2.4 140
  2LHB - 1MBD 1.4 137 6.0 1.4 135 1.6 137 1.5 137
  2LHB - 2HBG 1.9 133 6.0 2.0 128 2.1 130 2.0 132
  1MBD - 1MBA 1.9 143 6.0 1.9 142 1.8 141 1.9 143
  1MBA - 1ECD 1.9 136 8.0 1.9 133 2.0 134 2.0 136
  2HBG - 1ECD 2.4 129 6.5 2.6 129 2.6 125 2.5 129
Ten 'difficult' structures 1FXI a - 1UBQ 2.5 70 6.0 2.6 60 3.8 64 2.6 63
  1TEN - 3HHR b 1.7 87 6.0 1.9 86 1.9 87 1.8 87
  3HLA b - 2RHE 2.9 87 6.0 3.0 75 3.4 84 3.3 83
  2AZA a - 1PAZ 2.5 82 4.5 2.5 81 2.9 84 2.4 83
  1CEW i - lMOL a 2.3 83 6.5 2.3 81 2.3 81 2.2 82
  1CID - 2RHE 2.3 98 6.5 3.2 97 2.9 97 2.5 97
  1CRL - 1EDE 3.1 281 6.0 3.5 211 3.8 219 5.0 126
  2SIM - 1NSB a 2.9 322 6.0 3.3 291 3.0 275 2.9 292
  1BGE b - 2GMF a 3.3 110 7.5 3.3 94 3.9 107 3.3 104
  1TIE - 4FGF 2.4 115 6.0 3.1 114 2.9 116 2.7 115
Different folds 1NSB a - 1TIE 3.1 156 6.0 -   6.4 88 -  
  1NSB a - 4FGF 3.0 118 6.0 -   5.8 72 -  
  1FXI a - 1CEW i 2.9 56 6.0 -   7.2 56 -  
  1FXI a - 1MOL a 2.9 70 6.0 -   5.8 48 -  
Different Classes 1BGE b - 1TEN 2.8 82 6.0 -   7.4 40 -  
  1BGE b - 1PAZ 3.2 103 6.0 -   6.2 48 -  
  2GMF a - 1TEN 3.0 68 6.0 -   4.8 40 -  
Circular permutation 1LED - 1NLS 1.1 213 6.0 1.9 119 1.1 112 -  
  2PIA - 1AXJ 3.3 118 6.0 3.49 36 3.3 62 -