Table 2 Docking simulations on a rigid TF-DNA benchmark with 38 cases
From: High performance transcription factor-DNA docking with GPU computing
PDB | 200 simulation runs | 800 simulation runs | 1600 simulation runs | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
conformation with the lowest RMSD | conformation with the lowest energy | conformation with the lowest RMSD | conformation with the lowest energy | conformation with the lowest RMSD | conformation with the lowest energy | |||||||
RMSD (Å) | E docking | RMSD (Å) | E docking | RMSD (Å) | E docking | RMSD (Å) | E docking | RMSD (Å) | E docking | RMSD (Å) | E docking | |
1aay | 0.38 | -208.30 | 0.42 | -209.88 | 0.35 | -208.39 | 0.44 | -210.37 | 0.35 | -208.39 | 0.44 | -210.37 |
1an2 | 0.66 | -119.22 | 0.66 | -119.22 | 0.57 | -118.31 | 0.66 | -119.22 | 0.57 | -118.31 | 0.66 | -119.22 |
1jj4 | 0.39 | -127.55 | 0.54 | -129.26 | 0.38 | -128.13 | 0.52 | -129.42 | 0.30 | -127.97 | 0.56 | -129.73 |
1jt0 | 5.20 | -82.27 | 5.20 | -82.27 | 0.46 | -124.44 | 0.46 | -124.44 | 0.46 | -124.44 | 0.46 | -124.44 |
1lmb | 0.16 | -199.62 | 0.16 | -199.62 | 0.07 | -199.77 | 0.17 | -200.04 | 0.06 | -198.95 | 0.18 | -200.19 |
1qn4 | 0.17 | -313.59 | 0.40 | -315.47 | 0.16 | -312.87 | 0.41 | -316.10 | 0.16 | -312.87 | 0.39 | -316.35 |
1qpi | 4.47 | -78.92 | 4.47 | -78.92 | 4.47 | -78.92 | 4.47 | -78.92 | 3.42 | -80.24 | 3.42 | -80.24 |
1sax | 1.12 | 14.81 | 28.63 | -85.69 | 1.12 | 14.81 | 28.63 | -85.69 | 1.09 | 16.15 | 19.15 | -86.56 |
1tro | 13.88 | -57.73 | 16.76 | -81.33 | 13.68 | -60.80 | 20.82 | -81.43 | 13.68 | -60.81 | 20.84 | -81.71 |
1z9c | 1.02 | -67.71 | 32.24 | -124.23 | 1.02 | -67.71 | 32.22 | -124.68 | 0.98 | -67.40 | 32.22 | -124.68 |
1zs4 | 0.58 | -99.50 | 30.17 | -100.80 | 0.28 | -95.76 | 30.18 | -100.94 | 0.28 | -95.76 | 0.69 | -101.68 |
2ac0 | 0.22 | 125.31 | 14.40 | 103.80 | 0.22 | 125.31 | 14.40 | 103.15 | 0.21 | 123.26 | 14.45 | 103.06 |
2cgp | 0.69 | -162.09 | 0.83 | -165.63 | 0.69 | -162.60 | 0.83 | -165.63 | 0.68 | -162.92 | 0.83 | -165.63 |
2e1c | 4.08 | -47.43 | 6.03 | -65.54 | 1.03 | -58.02 | 6.05 | -65.72 | 1.03 | -58.02 | 6.05 | -65.72 |
2it0 | 10.10 | -84.19 | 13.91 | -88.21 | 10.10 | -84.19 | 13.99 | -88.93 | 7.02 | -64.61 | 13.91 | -89.00 |
2or1 | 1.05 | -200.25 | 1.61 | -209.88 | 0.90 | -199.81 | 1.63 | -210.06 | 0.86 | -199.78 | 1.62 | -210.64 |
2yvh | 19.38 | -79.05 | 36.64 | -97.66 | 17.29 | -67.95 | 35.64 | -97.98 | 10.69 | -62.60 | 35.64 | -97.98 |
3clc | 6.42 | -61.80 | 20.43 | -77.15 | 6.42 | -61.80 | 20.43 | -77.15 | 6.23 | -51.19 | 20.43 | -77.15 |
3dnv | 0.58 | -144.19 | 0.69 | -145.67 | 0.58 | -144.19 | 0.70 | -145.68 | 0.58 | -144.19 | 0.68 | -145.71 |
3e6c | 13.52 | -68.30 | 16.25 | -96.54 | 7.18 | -61.11 | 16.22 | -97.42 | 7.18 | -61.11 | 16.22 | -97.42 |
3gz6 | 3.68 | -40.08 | 36.98 | -43.99 | 2.34 | -42.74 | 4.38 | -44.12 | 2.34 | -42.74 | 4.39 | -44.18 |
1b01 | 0.95 | 4.05 | 10.57 | -9.36 | 0.95 | 4.05 | 10.57 | -9.36 | 0.95 | 4.05 | 10.61 | -9.41 |
1by4 | 0.43 | -186.88 | 0.43 | -186.88 | 0.40 | -185.19 | 0.42 | -186.99 | 0.40 | -185.19 | 0.42 | -187.09 |
1cma | 0.71 | -46.26 | 0.71 | -46.26 | 0.53 | -33.93 | 0.71 | -46.26 | 0.48 | -33.24 | 0.71 | -46.26 |
1gxp | 1.21 | -55.52 | 38.72 | -74.32 | 0.93 | -56.93 | 38.72 | -74.73 | 0.93 | -56.93 | 38.70 | -74.80 |
1h8a | 15.79 | -106.71 | 18.70 | -116.66 | 15.55 | -108.11 | 18.70 | -116.66 | 15.54 | -108.31 | 18.73 | -116.71 |
1hjc | 2.00 | -50.80 | 25.31 | -67.89 | 2.00 | -50.80 | 25.29 | -68.16 | 2.00 | -50.80 | 25.29 | -68.16 |
1r8d | 13.90 | -57.78 | 35.96 | -92.92 | 12.41 | -82.12 | 35.92 | -93.33 | 11.64 | -67.42 | 36.12 | -94.01 |
1rio | 23.98 | 60.74 | 60.65 | -43.07 | 23.95 | 61.05 | 60.65 | -43.16 | 23.95 | 61.05 | 60.58 | -43.44 |
1xpx | 1.27 | -56.51 | 20.96 | -73.48 | 1.21 | -56.52 | 20.96 | -73.48 | 1.20 | -56.85 | 20.96 | -73.48 |
1zme | 13.83 | -44.24 | 32.10 | -70.01 | 13.83 | -44.24 | 32.09 | -70.12 | 13.83 | -44.24 | 32.12 | -70.88 |
2bnw | 3.47 | -42.43 | 8.16 | -44.98 | 3.41 | -42.44 | 8.16 | -44.98 | 3.40 | -42.25 | 8.18 | -45.05 |
2c6y | 5.03 | -56.01 | 31.52 | -88.13 | 4.15 | -58.13 | 31.52 | -88.53 | 4.15 | -58.13 | 31.52 | -88.53 |
2fio | 18.40 | -52.54 | 43.65 | -137.99 | 18.40 | -52.54 | 33.45 | -1245.70 | 17.68 | -43.64 | 33.45 | -1245.70 |
2irf | 0.55 | -88.97 | 0.96 | -92.62 | 0.55 | -88.97 | 0.95 | -92.82 | 0.43 | -87.69 | 0.96 | -92.98 |
2rbf | 6.35 | -38.23 | 8.66 | -52.78 | 6.35 | -38.23 | 8.66 | -52.78 | 6.35 | -38.23 | 24.06 | -53.50 |
2zhg | 12.53 | -45.59 | 28.78 | -81.92 | 6.85 | -54.71 | 28.76 | -82.33 | 5.45 | -50.31 | 28.75 | -82.56 |
3hdd | 4.19 | -100.07 | 4.56 | -102.31 | 4.09 | -100.98 | 4.56 | -102.31 | 4.09 | -100.98 | 4.57 | -102.40 |