Table 1 Docking evaluation on 75 non-redundant TF-DNA complexes
From: High performance transcription factor-DNA docking with GPU computing
Conformation with the lowest RMSD | Conformation with the lowest energy | Number of Monte-Carlo runs | |||||||
|---|---|---|---|---|---|---|---|---|---|
ID | PDB ID | E docking | RMSD(Å) | E docking | RMSD(Å) | 200 | 400 | 800 | 1600 |
1 | 1a02 | 2483.21 | 11.72 | -87.22 | 22.51 | ||||
2 | 1a0a | -138.17 | 0.41 | -140.53 | 0.46 | x(x) | x(x) | x(x) | x(x) |
3 | 1akh | -194.5 | 0.15 | -195.44 | 0.17 | x(x) | x(x) | x(x) | |
4 | 1am9 | -246.58 | 0.1 | -248.37 | 0.11 | x(x) | x(x) | x(x) | x(x) |
5 | 1an4 | -50.06 | 8.05 | -96.87 | 13.65 | ||||
6 | 1b72 | -202.72 | 0.2 | -203.79 | 0.4 | x(x) | x(x) | x(x) | x(x) |
7 | 1bdt | -335.33 | 0.08 | -338.16 | 0.11 | x(x) | x(x) | x(x) | x(x) |
8 | 1cf7 | -123.5 | 0.22 | -125.81 | 0.37 | x(x) | x(x) | x(x) | x(x) |
9 | 1cma | -52.28 | 0.19 | -56.19 | 20.75 | x(x) | x(x) | x(x) | x(x) |
10 | 1d3u | -390.32 | 0.21 | -396.4 | 0.4 | x(x) | x(x) | x(x) | x(x) |
11 | 1d5y | -122.22 | 15.62 | -178.55 | 63.19 | ||||
12 | 1dh3 | -33.21 | 1.94 | -38.8 | 30.76 | ||||
13 | 1efa | -171.99 | 0.06 | -175.57 | 0.2 | x(x) | x(x) | x(x) | x(x) |
14 | 1g2d | -329.91 | 0.18 | -336.89 | 0.64 | x(x) | x(x) | x(x) | x(x) |
15 | 1gd2 | -192.36 | 0.08 | -195.4 | 0.13 | x(x) | x(x) | x(x) | x(x) |
16 | 1gxp | -200.25 | 0.14 | -205.16 | 0.22 | x(x) | x(x) | x(x) | x(x) |
17 | 1h6f | -195.97 | 0.09 | -195.97 | 0.09 | x(x) | |||
18 | 1h88 | -81.23 | 21.4 | -112.61 | 70.87 | ||||
19 | 1h9d | -181.85 | 0.21 | -185.43 | 0.28 | x(x) | x(x) | x(x) | x(x) |
20 | 1ic8 | -358.99 | 0.17 | -364.87 | 0.25 | x(x) | x(x) | x(x) | x(x) |
21 | 1je8 | -30.9 | 6.09 | -85.71 | 63.32 | ||||
22 | 1jfi | -320.51 | 0.21 | -324.72 | 0.26 | x(x) | x(x) | x(x) | x(x) |
23 | 1jj4 | -141.63 | 0.22 | -143.72 | 0.4 | x(x) | x(x) | x(x) | x(x) |
24 | 1jt0 | -275.84 | 0.09 | -279.95 | 0.14 | x(x) | x(x) | x(x) | x(x) |
25 | 1ku7 | -54.95 | 0.66 | -72.58 | 22.43 | x() | x() | x() | x() |
26 | 1l3l | -93.27 | 3.49 | -135.37 | 62.72 | ||||
27 | 1le5 | -466.48 | 0.2 | -470.46 | 0.22 | x(x) | x(x) | x(x) | x(x) |
28 | 1lq1 | -232.93 | 0.38 | -233.89 | 0.39 | x(x) | x(x) | x(x) | x(x) |
29 | 1mdm | -78.93 | 8.34 | -87.35 | 50.2 | ||||
30 | 1mdy | -131.3 | 0.12 | -133.91 | 0.23 | x(x) | x(x) | x(x) | x(x) |
31 | 1mnm | -232.86 | 0.1 | -234.38 | 0.16 | x(x) | x(x) | x(x) | x(x) |
32 | 1nkp | -225.91 | 0.19 | -226.15 | 0.19 | x(x) | x(x) | ||
33 | 1nlw | -260.52 | 0.43 | -261.85 | 0.47 | x(x) | x(x) | x(x) | x(x) |
34 | 1ozj | -87.62 | 0.4 | -89.39 | 0.53 | x(x) | x(x) | x(x) | x(x) |
35 | 1pp7 | -41.26 | 3.34 | -57.53 | 8.43 | ||||
36 | 1pue | -70.94 | 0.29 | -80.75 | 56.96 | x() | x() | x() | x() |
37 | 1puf | -269.14 | 0.42 | -271.22 | 0.5 | x(x) | x(x) | x(x) | x(x) |
38 | 1qne | -598.6 | 0.2 | -606.45 | 0.36 | x(x) | x(x) | x(x) | x(x) |
39 | 1qp9 | -220.62 | 0.17 | -221.97 | 0.17 | x(x) | x(x) | x(x) | x(x) |
40 | 1r8d | -73.99 | 11.58 | -106.13 | 35.66 | ||||
41 | 1rio | -179.09 | 0.08 | -180.44 | 0.15 | x(x) | x(x) | x(x) | x(x) |
42 | 1rzr | -123.71 | 0.72 | -142.16 | 37.7 | x() | x() | x() | |
43 | 1skn | -32.36 | 4.35 | -73.58 | 33.34 | ||||
44 | 1t2k | 100.11 | 0.96 | 96.65 | 0.98 | x(x) | x(x) | x(x) | x(x) |
45 | 1ttu | -57.09 | 1.7 | -78.09 | 30.8 | ||||
46 | 1u8b | -47.93 | 1.12 | -83.26 | 30.23 | ||||
47 | 1u8r | 595.89 | 0.76 | 262.38 | 98.73 | x() | x() | x() | x() |
48 | 1ysa | 3800.94 | 12.51 | -54.74 | 28.61 | ||||
49 | 1z9c | -160.1 | 0.21 | -194.41 | 75.44 | x() | x() | x() | x() |
50 | 1zme | -38.31 | 12.31 | -76.31 | 22.11 | ||||
51 | 1zrf | -155 | 0.25 | -156.66 | 0.25 | x(x) | x(x) | x(x) | x(x) |
52 | 1zs4 | -91.84 | 0.61 | -104.68 | 46.32 | x() | x() | x() | x() |
53 | 2as5 | -329 | 0.36 | -340.64 | 0.46 | x(x) | x(x) | x(x) | x(x) |
54 | 2c9l | -38.93 | 0.48 | -46.69 | 25.73 | x() | |||
55 | 2d5v | -193.42 | 0.42 | -196.68 | 0.5 | x(x) | x(x) | x(x) | x(x) |
56 | 2drp | -303.41 | 0.16 | -306.18 | 0.34 | x(x) | x(x) | x(x) | x(x) |
57 | 2er8 | -23.48 | 0.16 | -108.6 | 29.25 | x | x() | x() | x() |
58 | 2etw | -105.4 | 0.21 | -106.11 | 0.26 | x(x) | x(x) | x(x) | x(x) |
59 | 2fio | -51.12 | 18.49 | -146.84 | 46.95 | ||||
60 | 2gli | -194.58 | 0.18 | -197.61 | 0.33 | x(x) | x(x) | x(x) | x(x) |
61 | 2h27 | 47.97 | 0.2 | -86.91 | 23.1 | x() | x() | ||
62 | 2nll | -199.27 | 0.31 | -201.17 | 0.51 | x(x) | x(x) | x(x) | x(x) |
63 | 2ntc | -50.65 | 3.26 | -103.2 | 33.95 | ||||
64 | 2pi0 | 86.73 | 0.39 | 55.57 | 40.36 | x() | x() | x() | x() |
65 | 2ql2 | -136.32 | 0.9 | -140.33 | 1.02 | x() | x() | x() | x() |
66 | 2r1j | -262.07 | 0.27 | -263.47 | 0.55 | x(x) | x(x) | x(x) | x(x) |
67 | 2w7n | -86.31 | 0.33 | -91.12 | 34.7 | x() | x() | x() | x() |
68 | 2yvh | 192.78 | 0.48 | -46.35 | 54.44 | x() | x() | x() | x() |
69 | 3a5t | -91.62 | 0.18 | -91.89 | 0.19 | x(x) | x(x) | x(x) | |
70 | 3bs1 | -51.78 | 5.92 | -66.91 | 28.18 | ||||
71 | 3clc | -68.46 | 6.97 | -94.63 | 12.53 | ||||
72 | 3coq | -30.5 | 18.87 | -79.66 | 30.57 | ||||
73 | 3cro | -114.09 | 0.6 | -119.95 | 1.07 | x() | x() | x() | x() |
74 | 3d1n | -944.87 | 0.19 | -952.56 | 0.21 | x(x) | x(x) | x(x) | x(x) |
75 | 3dfx | -107.27 | 0.35 | -107.27 | 0.35 | x(x) | x(x) | ||
Total | 47(36) | 50(38) | 53(40) | 55(41) | |||||