Table 1

Markov clustering of PDB (as of 25 February 2003) at selected inflation (I) values. This version of PDB contains 2147 SCOP families and 4526 SCOP domains. There are 1340 SCOP families among the 6435 entries/IDs annotated with one SCOP family each, and 2621 SCOP domains among the 6430 entries/IDs annotated with one SCOP domain each.

Inflation =

1.00

1.10

2.00

3.00

4.00

5.00

Number of clusters (N ≥ 2)

761

773

906

952

976

998

pure clusters by SCOP family

427

433

424

404

393

384

with 1 SCOP family

380

383

386

369

360

353

with 2 SCOP families

36

39

35

33

31

29

with ≥ 2 SCOP families

11

11

3

2

2

2

most families in 1 cluster

8

7

3

3

3

3

Number of clusters (N ≥ 2)

761

773

906

952

976

998

pure clusters by SCOP domain

681

693

787

796

793

793

with 1 SCOP domain

358

359

445

460

467

474

with 2 SCOP domains

176

181

194

202

197

195

with ≥ 2 SCOP domains

147

153

148

134

129

124

most domains in 1 cluster

21

21

15

22

23

23

Number of families in all clusters (N ≥ 2)

831

831

817

814

814

812

with all members in 1 cluster

573

572

511

483

469

455

with all members in 2 clusters

150

146

169

174

177

181

with all members in 3 clusters

50

54

61

70

77

76

with all members in ≥ 3 clusters

58

59

76

87

91

100

most clusters 1 family occurs in

27

27

27

27

27

27

Number of domains in all clusters (N ≥ 2)

1852

1849

1796

1781

1771

1763

with all instances in 1 cluster

1743

1740

1665

1625

1597

1565

with all instances in 2 clusters

84

84

102

122

139

158

with all instances in ≥ 2 clusters

25

25

29

34

35

40

most clusters 1 domain occurs in

10

10

10

10

10

10

Harlow et al. BMC Bioinformatics 2004 5:45   doi:10.1186/1471-2105-5-45