Table 14 The Docking Results of DoBi and ZDOCK on Benchmark v4.0
From: Protein-protein binding site identification by enumerating the configurations
DoBi1000 | ZDOCK | DoBi1000 | ZDOCK | DoBi1000 | ZDOCK | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PDB | iRmsda | F l b | F r c | iRmsd | F l | F r | PDB | iRmsd | F l | F r | iRmsd | F l | F r | PDB | iRmsd | F l | F r | iRmsd | F l | F r |
1bvk | 1.24 | 71.8 | 72.7 | 1.72 | 71.4 | 80.0 | 1jps | 4.27 | 66.7 | 62.8 | 2.26 | 78.3 | 82.6 | 1gla | 6.51 | 77.3 | 72.4 | 3.76 | 70.3 | 72.0 |
2sni | 1.49 | 92.9 | 82.8 | 2.55 | 90.0 | 78.3 | 1yvb | 4.44 | 71.0 | 51.3 | 1.61 | 82.4 | 91.3 | 1acb | 6.55 | 78.8 | 78.0 | 2.61 | 93.8 | 82.6 |
1j2j | 1.52 | 80.0 | 83.9 | 2.18 | 66.7 | 56.4 | 1avx | 4.54 | 66.7 | 70.2 | 1.67 | 73.3 | 88.5 | 2i25 | 6.57 | 46.2 | 68.6 | 1.40 | 80.0 | 72.0 |
1wq1 | 1.60 | 88.5 | 76.9 | 1.82 | 77.6 | 69.2 | 1fq1 | 4.54 | 62.9 | 76.5 | 8.05 | 42.4 | 50.0 | 1z0k | 6.60 | 72.7 | 55.2 | 2.29 | 90.3 | 75.0 |
1rv6 | 1.68 | 80.0 | 88.2 | 1.43 | 86.7 | 83.3 | 1e6e | 4.58 | 67.9 | 60.9 | 1.11 | 85.0 | 85.7 | 1fc2 | 6.88 | 59.5 | 73.7 | 3.53 | 69.0 | 58.1 |
1z5y | 1.70 | 82.9 | 89.5 | 1.69 | 85.7 | 86.4 | 2cfh | 4.58 | 63.8 | 66.7 | 1.53 | 84.2 | 76.6 | 1oph | 6.97 | 72.2 | 80.8 | 2.00 | 70.6 | 58.1 |
1n8o | 1.73 | 81.5 | 89.9 | 2.28 | 82.9 | 78.7 | 1oyv | 4.61 | 85.7 | 66.7 | 2.12 | 83.0 | 84.1 | 1jmo | 7.01 | 80.0 | 66.6 | 18.99 | 36.4 | 0 |
1buh | 1.98 | 82.4 | 70.3 | 1.12 | 87.5 | 96.3 | 1kkl | 4.74 | 36.4 | 57.9 | 27.92 | 0 | 0 | 1he1 | 7.07 | 90.0 | 89.7 | 2.02 | 80.9 | 70.6 |
2j0t | 2.16 | 57.1 | 48.8 | 4.86 | 59.1 | 56.1 | 1bvn | 4.82 | 74.5 | 48.0 | 1.72 | 87.5 | 82.9 | 1xd3 | 7.08 | 66.7 | 72.2 | 0.45 | 96.3 | 93.8 |
1qa9 | 2.20 | 47.6 | 61.1 | 4.00 | 51.9 | 64.5 | 1gp2 | 4.83 | 86.1 | 84.4 | 3.39 | 56.2 | 92.9 | 2oor | 7.17 | 64.5 | 68.7 | 3.14 | 75.0 | 63.0 |
1gcq | 2.27 | 90.9 | 75.3 | 5.19 | 71.0 | 64.0 | 1ktz | 4.84 | 80.0 | 69.6 | 3.68 | 91.7 | 63.6 | 1ibr | 7.23 | 55.3 | 63.4 | 9.83 | 50.6 | 33.8 |
1b6c | 2.32 | 71.0 | 77.8 | 2.63 | 82.9 | 88.4 | 2g77 | 4.84 | 68.1 | 61.6 | 1.52 | 94.5 | 86.2 | 1ak4 | 7.25 | 52.2 | 52.6 | 4.28 | 85.7 | 90.0 |
2b42 | 2.35 | 78.6 | 88.2 | 1.36 | 94.1 | 87.7 | 2btf | 4.86 | 71.7 | 66.7 | 2.48 | 74.4 | 80.0 | 1vfb | 7.27 | 48.9 | 50.0 | 2.30 | 74.3 | 72.2 |
2a5t | 2.38 | 82.1 | 78.8 | 4.36 | 52.0 | 40.0 | 1jiw | 4.86 | 79.5 | 81.5 | 5.22 | 56.5 | 66.7 | 1k4c | 7.29 | 70.3 | 44.4 | 1.47 | 81.2 | 97.7 |
1gpw | 2.45 | 79.1 | 64.0 | 1.51 | 81.6 | 78.4 | 1gxd | 4.88 | 73.3 | 62.5 | 3.41 | 80.9 | 64.9 | 2vdb | 7.31 | 74.1 | 64.8 | 1.28 | 90.5 | 100 |
1fle | 2.47 | 78.6 | 73.2 | 4.01 | 74.1 | 44.0 | 1f51 | 4.89 | 70.6 | 68.6 | 2.40 | 66.7 | 68.3 | 1gl1 | 7.42 | 96.3 | 86.8 | 1.55 | 81.2 | 83.3 |
2ido | 2.48 | 87.5 | 82.8 | 5.09 | 71.4 | 80.0 | 1jzd | 4.92 | 75.0 | 71.0 | 2.67 | 76.2 | 73.7 | 1syx | 7.49 | 75.0 | 75.7 | 4.81 | 64.5 | 85.0 |
1fqj | 2.49 | 79.1 | 66.7 | 13.13 | 16.7 | 26.3 | 1pvh | 4.94 | 54.5 | 79.0 | 1.92 | 75.0 | 88.9 | 1eer | 7.49 | 66.7 | 53.8 | 7.90 | 58.1 | 54.5 |
2hrk | 2.51 | 100 | 88.2 | 2.06 | 80.0 | 70.6 | 1m10 | 4.96 | 75.9 | 60.0 | 9.42 | 36.1 | 29.8 | 2oob | 7.58 | 53.3 | 71.0 | 5.38 | 81.8 | 81.8 |
1dqj | 2.52 | 79.2 | 91.3 | 8.31 | 53.7 | 35.9 | 2abz | 4.99 | 54.8 | 58.6 | 3.73 | 89.7 | 84.6 | 1jtg | 7.69 | 78.1 | 76.7 | 1.39 | 81.5 | 80.7 |
1ezu | 2.53 | 84.7 | 74.7 | 2.38 | 94.3 | 78.9 | 1bkd | 5.04 | 81.1 | 77.1 | 7.33 | 59.6 | 53.5 | 1nsn | 7.91 | 73.9 | 74.4 | 4.82 | 42.1 | 82.1 |
1k5d | 2.54 | 90.4 | 78.4 | 2.51 | 73.0 | 70.0 | 1i2m | 5.06 | 85.7 | 64.5 | 2.21 | 77.4 | 83.6 | 1zm4 | 7.98 | 43.6 | 31.4 | 2.44 | 66.7 | 56.0 |
2qfw | 2.61 | 93.3 | 87.5 | 1.58 | 88.9 | 73.7 | 1e6j | 5.06 | 54.1 | 50.0 | 1.57 | 100 | 100 | 1udi | 8.08 | 51.1 | 50.0 | 1.42 | 88.9 | 86.7 |
2ayo | 2.61 | 73.4 | 68.9 | 1.85 | 92.6 | 88.9 | 3sgq | 5.09 | 81.8 | 77.3 | 2.19 | 84.4 | 84.4 | 2ot3 | 8.11 | 76.3 | 71.6 | 4.40 | 64.2 | 73.7 |
2hle | 2.63 | 55.6 | 58.8 | 3.52 | 72.7 | 61.2 | 1ewy | 5.13 | 65.0 | 66.7 | 2.47 | 73.2 | 77.8 | 3cph | 8.29 | 73.2 | 59.3 | 3.91 | 66.7 | 66.7 |
1zhh | 2.67 | 66.7 | 70.4 | 9.28 | 27.5 | 45.6 | 1kxp | 5.13 | 62.0 | 78.8 | 2.00 | 80.0 | 66.7 | 1eaw | 8.31 | 95.2 | 85.3 | 1.34 | 92.9 | 92.3 |
1ay7 | 2.73 | 74.3 | 61.5 | 4.64 | 66.7 | 40.7 | 2c0l | 5.14 | 84.9 | 71.8 | 4.36 | 45.7 | 41.9 | 1tmq | 8.53 | 57.2 | 61.6 | 2.42 | 90.6 | 82.8 |
1f6m | 2.76 | 84.0 | 83.3 | 12.24 | 26.1 | 19.2 | 2hmi | 5.14 | 60.0 | 46.1 | 26.99 | 73.9 | 0 | 1efn | 8.61 | 66.7 | 64.3 | 6.62 | 63.6 | 41.7 |
2a9k | 2.80 | 89.7 | 81.0 | 5.67 | 62.1 | 37.8 | 1pxv | 5.17 | 83.9 | 86.5 | 3.81 | 61.9 | 62.7 | 1n2c | 8.66 | 86.4 | 78.9 | 3.21 | 75.7 | 92.8 |
1oc0 | 2.82 | 77.4 | 57.2 | 2.95 | 75.9 | 75.9 | 1sbb | 5.18 | 75.9 | 76.9 | 8.23 | 21.4 | 37.8 | 2fju | 8.75 | 76.6 | 60.0 | 1.47 | 81.5 | 81.5 |
1i4d | 2.97 | 71.1 | 65.3 | 1.97 | 68.4 | 64.9 | 1us7 | 5.18 | 55.6 | 76.2 | 1.17 | 88.0 | 84.6 | 1r0r | 8.91 | 76.5 | 59.0 | 2.10 | 80 | 82.4 |
2o8v | 2.97 | 66.6 | 57.1 | 2.76 | 84.2 | 66.6 | 2jel | 5.25 | 80.0 | 77.3 | 2.40 | 93.3 | 79.1 | 1wej | 8.96 | 42.9 | 53.3 | 24.79 | 5.7 | 0 |
1wdw | 3.02 | 73.8 | 70.2 | 1.54 | 94.6 | 87.5 | 1fcc | 5.25 | 66.7 | 47.6 | 11.33 | 29.4 | 32.5 | 1s1q | 9.13 | 93.3 | 88.9 | 1.76 | 97.0 | 72.7 |
1mq8 | 3.02 | 71.8 | 66.7 | 6.72 | 85.7 | 29.6 | 1lfd | 5.27 | 62.9 | 50.0 | 4.94 | 70.0 | 64.3 | 2o3b | 9.15 | 48.0 | 48.6 | 14.16 | 44.4 | 32.0 |
2z0e | 3.02 | 75.6 | 80.0 | 4.24 | 69.6 | 58.2 | 2j7p | 5.38 | 66.7 | 64.7 | 6.89 | 50.9 | 59.0 | 1e4k | 9.42 | 75.9 | 86.2 | 15.2 | 21.7 | 12.8 |
1nw9 | 3.02 | 70.6 | 66.7 | 3.19 | 78.8 | 68.6 | 1akj | 5.44 | 66.7 | 79.3 | 5.55 | 61.5 | 74.1 | 1cgi | 9.48 | 80.0 | 77.4 | 1.59 | 97.4 | 89.3 |
1ofu | 3.13 | 66.7 | 82.4 | 2.05 | 81.2 | 84.8 | 1ijk | 5.46 | 60.6 | 44.5 | 1.86 | 91.7 | 74.3 | 1clv | 9.48 | 77.1 | 66.6 | 1.58 | 88.9 | 87.0 |
1i9r | 3.20 | 62.1 | 59.2 | 21.89 | 37.5 | 0 | 2nz8 | 5.49 | 72.8 | 75.0 | 2.87 | 82.6 | 75.8 | 7cei | 9.51 | 54.5 | 48.5 | 0.88 | 88.0 | 88.9 |
1e96 | 3.21 | 96.5 | 84.6 | 2.98 | 55.2 | 63.2 | 1h9d | 5.49 | 62.9 | 80.0 | 1.88 | 84.4 | 81.1 | 2vis | 9.57 | 81.0 | 91.4 | 22.23 | 0 | 0 |
1t6b | 3.22 | 71.2 | 70.2 | 1.19 | 85.0 | 90.9 | 1rlb | 5.50 | 76.2 | 58.8 | 14.71 | 26.7 | 23.8 | 1bgx | 9.90 | 78.3 | 80.0 | 11.09 | 50.5 | 27.2 |
2oul | 3.30 | 64.9 | 65.5 | 1.97 | 80.0 | 86.8 | 1bj1 | 5.59 | 83.3 | 85.7 | 2.11 | 92.7 | 88.0 | 1d6r | 10.54 | 41.0 | 66.6 | 12.68 | 25.0 | 22.9 |
1ahw | 3.36 | 45.2 | 57.1 | 1.86 | 88.9 | 89.4 | 1r6q | 5.59 | 50.0 | 78.6 | 5.20 | 47.4 | 53.3 | 2ajf | 10.60 | 52.4 | 51.1 | 3.57 | 72.3 | 69.6 |
1y64 | 3.44 | 94.1 | 88.9 | 15.37 | 31.6 | 21.6 | 1qfw | 5.61 | 48.0 | 57.2 | 1.50 | 93.3 | 77.8 | 1ml0 | 10.69 | 54.0 | 42.4 | 1.29 | 82.6 | 86.8 |
1ffw | 3.44 | 42.1 | 66.7 | 3.91 | 56.0 | 57.1 | 2uuy | 5.66 | 66.7 | 62.3 | 4.20 | 44.5 | 76.2 | 1k74 | 10.73 | 39.1 | 20.2 | 1.63 | 76.6 | 80.8 |
1grn | 3.46 | 78.8 | 70.3 | 1.81 | 69.4 | 70.0 | 1iqd | 5.66 | 64.9 | 70.4 | 1.26 | 94.4 | 80.0 | 1dfj | 11.14 | 48.3 | 35.5 | 1.29 | 87.9 | 82.4 |
2pcc | 3.52 | 65.4 | 66.7 | 5.34 | 76.5 | 43.3 | 2oza | 5.71 | 60.5 | 69.2 | 8.49 | 40.8 | 28.9 | 1kac | 11.24 | 74.1 | 42.9 | 3.22 | 87.8 | 85.0 |
1hcf | 3.57 | 75.9 | 71.4 | 0.95 | 90.9 | 86.5 | 1fak | 5.73 | 71.4 | 86.3 | 7.73 | 40.0 | 44.9 | 1xu1 | 11.36 | 87.5 | 78.8 | 1.54 | 89.7 | 80.0 |
1a2k | 3.57 | 75.7 | 50.0 | 1.91 | 55.8 | 53.7 | 1de4 | 5.76 | 53.9 | 70.0 | 1.77 | 80.0 | 78.4 | 1mah | 11.55 | 86.9 | 73.5 | 1.87 | 86.5 | 83.6 |
1jwh | 3.61 | 66.7 | 75.6 | 1.28 | 80.0 | 66.7 | 1zgi | 5.82 | 90.9 | 88.2 | 1.79 | 78.3 | 85.7 | 1he8 | 11.95 | 58.3 | 56.3 | 2.38 | 60.0 | 64.3 |
1atn | 3.70 | 72.3 | 83.3 | 4.74 | 79.1 | 80.0 | 1azs | 5.86 | 62.9 | 75.9 | 1.18 | 84.2 | 83.3 | 1fsk | 11.99 | 61.1 | 62.8 | 1.15 | 91.9 | 90.5 |
2sic | 3.76 | 72.2 | 76.4 | 0.94 | 96.3 | 90.9 | 1hia | 5.91 | 66.7 | 56.1 | 12.4 | 23.0 | 28.6 | 1h1v | 14.13 | 20.4 | 38.9 | 16.72 | 18.2 | 20.7 |
1ppe | 3.83 | 76.9 | 83.3 | 1.42 | 86.7 | 93.5 | 1mlc | 6.18 | 54.2 | 71.9 | 1.52 | 80.0 | 78.9 | 1xqs | 14.27 | 37.2 | 23.3 | 1.67 | 79.1 | 85.7 |
1klu | 3.94 | 83.7 | 90.9 | 11.1 | 27.5 | 43.2 | 2fd6 | 6.20 | 63.0 | 53.3 | 4.34 | 75.9 | 43.4 | 1jk9 | 15.43 | 84.4 | 74.4 | 2.16 | 82.9 | 73.2 |
1zli | 3.97 | 87.1 | 71.4 | 12.25 | 43.2 | 28.6 | 4cpa | 6.21 | 62.1 | 72.0 | 1.74 | 80.0 | 81.0 | 1ghq | 16.12 | 68.3 | 57.7 | 22.15 | 0 | 48.0 |
3d5s | 3.97 | 70.0 | 72.3 | 2.08 | 81.1 | 84.2 | 1nca | 6.25 | 64.5 | 71.0 | 1.38 | 90.2 | 87.0 | 1r8s | 20.83 | 12.6 | 57.7 | 6.48 | 49.2 | 54.5 |
2b4j | 4.00 | 82.4 | 83.7 | 10.33 | 35.7 | 28.6 | 1f34 | 6.36 | 59.3 | 61.5 | 1.94 | 84.8 | 83.6 | 1kxq | 21.12 | 75.0 | 80.0 | 1.18 | 84.6 | 93.5 |
2i9b | 4.18 | 80.0 | 79.2 | 5.58 | 78.3 | 42.1 | 1ib1 | 6.42 | 64.8 | 71.4 | 5.89 | 53.1 | 46.4 | 2hqs | 26.33 | 10.5 | 22.6 | 12.37 | 15.0 | 29.1 |
2mta | 4.18 | 82.1 | 86.5 | 1.64 | 84.6 | 82.4 | 3bp8 | 6.49 | 61.0 | 63.2 | 4.02 | 57.9 | 68.8 | 1ira | 28.13 | 31.8 | 25.0 | 16.42 | 36.5 | 28.9 |
2h7v | 4.19 | 72.2 | 81.2 | 2.64 | 85.7 | 80.0 | ||||||||||||||