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Table 2 Known circular permutation results

From: Topology independent protein structural alignment

Protein 1

Protein 2

Us

MASS

OPAAS

SAMO

Topofit

PDB(Length)

PDB(Length)

N

R

p

N

R

N

R

N

R

N

R

1rinA(180)

2cna_(237)

152*

0.875

10-6

164*

1.2

167*

1.48

174*

1.581

152*

1.09

1glh_(214)

1cpn_(208)

192*

1.163

10-5

206*

0.49

No

solution

170*

3.283

206*

0.49

1exg_(110)

1tul_(102)

74*

1.485

10-4

60*

1.9

No

solution

93*

2.88

52*

1.79

1rhgA(145)

1bcfA(158)

118*

1.500

10-4

106*

1.7

63*

2.12

126*

2.309

109*

1.4

1ihwA(52)

1sso_(62)

46*

0.502

10-3

39*

1.7

No

solution

48*

2.713

35*

1.47

  1. Comparison of our alignment results with that of MASS, OPAAS, SAMO, and Topofit for known circular permutations. Each method detected the circular permutations. Our method normally returns more equivalent residues at a lower RMSD. N indicates the number of aligned residues. An * next to the number of aligned residues indicates that a circular permutation was found. R indicates the cRMSD of the alignment. p indicates the p-value of our alignment.