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Table 1 Domain-domain assembly with pyDockTET using homology models or X-ray structures of the interacting domains

From: Structural assembly of two-domain proteins by rigid-body docking

linker length

domain-domain PDBa

docking from cryst.b

Docking from modelsc

  

pyDock

pyDockTET

pyDock

pyDockTET

2

1b8p_A_158_159

1 (1.3)

1 (6.8)

6 (4.5)

6 (4.5)

4

1ar4_A_84_87

68 (2.2)

39 (2.2)

15 (5.5)

2 (5.5)

 

1aw7_A_93_96

1 (2.2)

1 (2.2)

1 (3.2)

1 (3.2)

 

1ffu_F_176_179

1 (1.9)

1 (1.9)

98 (9.6)

121 (9.6)

5

1b06_A_93_97

11 (3.9)

1 (3.9)

3 (4.2)

2 (7.5)

6

1dlu_B_263_268

1 (1.8)

1 (1.8)

1 (5.1)

1 (9.2)

7

1ca1_-_251_257

301 (4.8)

10 (4.8)

415 (7.7)

22 (7.8)

 

1e5m_A_251_257

1 (1.3)

1 (1.3)

1 (3.6)

1 (3.6)

 

1gk8_C_147_153

-

-

-

-

8

1j3n_A_244_251

1 (1.9)

1 (5.6)

1 (2.0)

1 (5.2)

9

1ee0_A_234_242

4 (8.1)

2 (8.1)

1 (2.9)

1 (2.9)

 

1nez_A_180_188

-

-

803 (9.1)

101 (9.1)

 

1s9v_B_88_96

-

-

-

-

11

1etp_B_90_100

809 (7.4)

204 (7.4)

1303 (9.8)

437 (9.8)

12

1onq_A_182_193

-

-

-

-

13

1edh_B_100_112

-

-

-

-

14

1hnf_-_97_110

-

-

-

-

 

1mb8_A_173_186

-

-

1 (7.2)

1 (7.2)

15

1jk8_B_88_102

-

-

-

-

16

1k2d_B_87_102

-

-

-

-

  1. a The name of the structure is shown with the format: (PDB ID)_(chain name)_(the first residue of the linker)_(the last residue of the linker)
  2. b The best ranking of any acceptable solution from docking the crystal structures. RMSD (Å) of the second domain is shown in brackets. '-' means that there is no acceptable solutions (≤ 10Å) generated by ZDOCK.
  3. c The best ranking of any acceptable solution from docking the modelled structures. RMSD (Å) of the second domain is shown in brackets. '-' means that there is no acceptable solutions (≤ 10Å) generated by ZDOCK.