Table 2

Results from different programs for difficult structure pairs

pair

PDB ID

PDB ID

Chimera

TOPOFIT

CE

CE/MA

1

3chy

2fox

88/2.2

19/0.7

108/3.6

93/2.6

2

2aza A

1paz

79/2.0

72/1.7

84/2.9

81/2.4

3

1cew I

1mol A

73/1.9

73/1.6

81/2.3

78/1.9

4

1cid

2rhe

90/2.0

69/1.5

97/2.9

88/1.9

5

1crl

1ede

184/2.5

143/1.9

219/3.8

183/2.3

6

2sim

1nsb A

257/2.6

207/2.0

275/3.0

266/2.5

7

1ten

3hhr B

82/1.3

81/1.4

87/1.9

85/1.6

8

1tie

4fgf

73/2.2

88/1.6

116/2.9

105/2.1

9

2snv

5ptp

118/2.3

83/1.8

130/3.1

118/2.4

10

1gp1 A

2trx A

89/1.8

96/1.6

64/5.2

54/2.7

Results are of the form N/RMSD, where N is the number of residue pairs matched and RMSD is the corresponding alpha-carbon root-mean-square deviation. Chimera: results from using MatchMaker and then Match -> Align with default settings, as reported under MM-default in Table 1. TOPOFIT [31] results were obtained using the web server [35]. CE [26] results were obtained using the web server [34] with default settings. CE/MA: equivalences obtained by using Match -> Align with cutoff 5.0 angstroms on the superpositions from CE.

Meng et al. BMC Bioinformatics 2006 7:339   doi:10.1186/1471-2105-7-339