Skip to main content

Table 1 Superposition results of protein systems with conformational changes using the LMS fit

From: Using least median of squares for structural superposition of flexible proteins

Protein system

PDB1

PDB2

RMSD

#Res1

#Subset

Core%2

Time(s)

ERα

3erd

3ert

4.9

244

203

83.2%

0.28

RAN

1byu

1rrp

14.4

200

141

70.5%

0.19

Myosin

1b7t

1dfk

13.0

720

403

56.0%

0.58

Calmodulin

1cll

1ctr

14.7

138

72

52.2%

0.09

Topo II

1bgw

1bjt

18.4

665

389

58.5%

0.55

Pneumolysin

2bk1

2bk2

21.8

435

139

32.0%

0.39

  1. 1 "#Res" is the number of atom pairs used for superposition by removing any inappropriate residues.
  2. 2 "Core%" is the proportion of the core region that belongs to the original point set.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us