Table 2 Rigid TF-DNA docking benchmark

Name

PDB

TF-DNA Unit Chains

ID

Res. (Å)

SCOP

Protein

Oligo_state

DNA

NRBC ^b

BSA(Å ² ) ^c

ZIF268

1aay

1.60

g.37.1.1

A

Monomer

B, C

13

960.81

Max

1an2

2.90

a.38.1.1

A, C

Homodimer

B, D

10

933.75

Papillomavirus E2

1jj4

2.40

d.58.8.1

A, B

Heterodimer

C, D

10

839.96

QacR

1jt0^a

2.90

a.4.1.9

B, D

Homodimer

E, F

12

1085.51

Lambda repressor

1lmb

1.80

a.35.1.2

3, 4

Homodimer

1, 2

10

1105.4

TATA-binding

1qn4

1.86

d.129.1.1

B

Monomer

E, F

15

1107.51

Tet repressor

1qpi

2.50

a.4.1.9

A, C

Homodimer

B, M

14

973.49

MecI

1sax

2.80

a.4.5.39

A, B

Homodimer

C, D

12

1130.16

Trep repressor

1tro^a

1.90

a.4.12.1

A, C

Homodimer

I, J

12

1243.06

OhrR

1z9c

2.64

a.4.5.28

C, D

Homodimer

I, J

12

1669.81

Easy

Phi lambda phage cII

1zs4

1.70

a.39.1.9

A, B, C, D

HT^d

U, T

14

1043.06

p53

2ac0

1.80

b.2.5.2

A, B, C, D

HT^d

E, F, G, H

21

1921.76

CAP

2cgp

2.20

a.4.5.4

A, F

Homodimer

B, C, D, E

10

944.43

LRP/ASNC family protein

2e1c

2.10

a.4.5.32

A, F

Homodimer

B, D

11

803.23

IdeR

2it0^a

2.60

a.4.5.24

C, D

Homodimer

E, F

11

1123.8

Phi 434 repressor

2or1

2.50

a.35.1.2

R, L

Homodimer

A, B

17

1021.78

CgmR

2yvh^a

2.50

N/A

C, D

Homodimer

E, F, G, H

10

1056.55

Controller protein

3clc^a

2.80

a.35.1.3

C, D

Homodimer

E, F

14

1002.57

HipB

3dnv

2.68

N/A

B, C

Homodimer

E, T

10

990.24

CprK

3e6c

1.80

a.4.5.4

C, D

Homodimer

A, B, E, F

12

1059.42

NrtR

3gz6

2.90

N/A

A, B

Homodimer

C, D

15

1845.4

CopG repressor

1b01

2.56

a.43.1.3

A, B

Homodimer

E, F

5

573.31

RXR-alpha

1by4

2.10

g.39.1.2

A, B

Homodimer

E, F

8

1031.94

Met repressor

1cma

2.80

a.43.1.5

A, B

Homodimer

C, D

4

693.13

PhoB

1gxp^a

2.50

a.4.6.1

A

Monomer

C, D

7

739.09

Myb

1h8a^a

2.23

a.4.1.3

C

Monomer

D, E

8

738.59

AML1 Runt domain

1hjc

2.65

b.2.5.6

D

Monomer

E, F

6

540.76

MtaN

1r8d

2.70

a.6.1.3

A, B

Homodimer

C, D

8

1338.92

Hard

Sigma subunit domain 4

1rio^a

2.30

a.4.13.2

H

Monomer

U, T

6

423.27

Prospero

1xpx

2.80

a.4.1.1

A

Monomer

C, D

3

325.79

Put3

1zme

2.50

g.38.1.1

C, D

Homodimer

A, B

5

1211.56

Omega repressor

2bnw

2.45

a.43.1.4

A, B

Homodimer

E, F

4

519.26

ILF

2c6y

2.40

a.4.5.14

A

Monomer

C, D

8

814.94

Phi 29 protein p4

2fio

2.70

N/A

A, B

Homodimer

C, D

4

903.33

IRF-2

2irf^a

2.20

a.4.5.23

L

Monomer

C, D

6

668.45

PutA

2rbf

2.25

N/A

A, B

Homodimer

C, D

8

614.12

SoxR

2zhg

2.80

a.6.1.3

A, D

Homodimer

B, C

6

869.73

Engrailed homeodomain

3hdd^a

2.20

a.4.1.1

A

Monomer

C, D

4

524.73