Table 1 Flexible TF-DNA docking benchmark

PDB

TF-DNA Unit Chains

NRBC ^b

PDB

Res.(Å)

Chains

RMSD _u (Å) ^e

RMSD _c (Å) ^e

Name

ID

Res.(Å)

SCOP

Protein

Oligo_state

DNA

CopG repressor

1b01

2.56

a.43.1.3

A, B

Homodimer

E, F

5

2cpg

1.60

A, B

0.511

0.460

PhoB

1gxp^a

2.50

a.4.6.1

A

Monomer

C, D

7

1gxq

2.00

A

1.622

1.622

AML1 Runt domain

1hjc

2.65

b.2.5.6

D

Monomer

E, F

6

1ean

1.70

A

1.056

1.056

Papillomavirus E2

1jj4

2.40

d.58.8.1

A, B

Heterodimer

C, D

10

1f9f

1.90

C, D

0.949

1.484

TATA-binding protein

1qn4

1.86

d.129.1.1

B

Monomer

E, F

15

1vok

2.10

B

0.934

0.934

Tet repressor

1qpi

2.50

a.4.1.9

A, C

Homodimer

B, M

14

2tct

2.10

A, B

2.061

1.359

MtaN

1r8d

2.70

a.6.1.3

A, B

Homodimer

C, D

8

1jbg

2.75

A, B

2.107

1.368

Sigma subunit domain 4

1rio^a

2.30

a.4.13.2

H

Monomer

U, T

6

1ku3

1.80

A

1.405

1.405

Easy

MecI

1sax

2.80

a.4.5.39

A, B

Homodimer

C, D

12

1okr

2.40

A, B

1.718

1.586

CAP

2cgp

2.20

a.4.5.4

A, F

Homodimer

B, C, D, E

10

1i5z

1.90

A, B

1.652

1.919

LRP/ASNC family protein

2e1c

2.10

a.4.5.32

A, F

Homodimer

B, D

12

2zny

2.59

A, B

1.339

1.184

IdeR

2it0^a

2.60

a.4.5.24

C, D

Homodimer

E, F

11

2isy

1.96

A, B

0.476

0.489

Phi 434 repressor

2or1

2.50

a.35.1.2

R, L

Homodimer

A, B

17

1r69^c

2.00

A, B

0.570

0.493

PutA

2rbf

2.25

N/A

A, B

Homodimer

C, D

8

2gpe

1.90

A, B

0.798

0.571

SoxR

2zhg

2.80

a.6.1.3

A, D

Homodimer

B, C

6

2zhh

3.20

A, B

1.749

1.467

Controller protein

3clc^a

2.80

a.35.1.3

C, D

Homodimer

E, F

14

3fya

3.00

A, B

0.834

0.809

CprK

3e6c

1.80

a.4.5.4

C, D

Homodimer

A, B, E, F

12

3e5u

1.83

A, B

1.060

0.906

NrtR

3gz6

2.90

N/A

A, B

Homodimer

C, D

15

3gz5

2.20

A, B

0.853

0.726

Max

1an2

2.90

a.38.1.1

A, C

Homodimer

B, D

10

1r05^d

N/A

A, B

8.074

4.767

RXR-alpha

1by4

2.10

g.39.1.2

A, B

Homodimer

E, F

8

1rxr^{c, d}

N/A

A, B

4.637

2.326

Met repressor

1cma

2.80

a.43.1.5

A, B

Homodimer

C, D

4

1cmc

1.80

A, B

2.232

2.313

Myb

1h8a^a

2.23

a.4.1.3

C

Monomer

D, E

8

1gv2

1.68

A

9.153

9.153

QacR

1jt0^a

2.90

a.4.1.9

B, D

Homodimer

E, F

12

1jt6

2.54

D, E

2.924

1.650

Lambda repressor

1lmb

1.80

a.35.1.2

3, 4

Homodimer

1, 2

10

1lrp

3.20

A, B

32.342

0.928

Trp repressor

1tro^a

1.90

a.4.12.1

A, C

Homodimer

I, J

12

1p6z

1.67

N, R

3.095

1.427

Prospero

1xpx

2.80

a.4.1.1

A

Monomer

C, D

3

1mij

2.05

A

0.519

0.519

Hard

OhrR

1z9c

2.64

a.4.5.28

C, D

Homodimer

I, J

12

1z91

2.50

A, B

2.521

1.919

Put3

1zme

2.50

g.38.1.1

C, D

Homodimer

A, B

5

1ajy^d

N/A

A, B

9.326

8.725

Phi lambda phage cII

1zs4

1.70

a.35.1.9

A, B, C, D

HT^f

U, T

14

1zpq

2.80

A, B, C, D

4.947

2.679

p53

2ac0

1.80

b.2.5.2

A, B, C, D

HT^f

E, F, G, H

21

2j1y

1.69

A, B, C, D

25.325

0.932

Omega repressor

2bnw

2.45

a.43.1.4

A, B

Homodimer

E, F

4

1irq

3.50

A, B

0.887

1.049

ILF

2c6y

2.40

a.4.5.14

A

Monomer

C, D

8

1jxs^d

N/A

A

2.830

2.830

Phi 29 protein p4

2fio

2.70

N/A

A, B

Homodimer

C, D

4

2fip

2.00

C, D

0.679

0.496

IRF-2

2irf^a

2.20

a.4.5.23

L

Monomer

C, D

6

1irf^d

N/A

A

3.459

3.459

CgmR

2yvh^a

2.50

N/A

C, D

Homodimer

E, F, G, H

10

2yve

1.40

A, B

2.663

1.599

HipB

3dnv

2.68

N/A

B, C

Homodimer

E, T

10

2wiu

2.35

B, D

3.511

2.925

Engrailed homeodomain

3hdd^a

2.20

a.4.1.1

A

Monomer

C, D

4

1enh

2.10

A

0.716

0.716