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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  
  1. aC α iRMSD between the configuration by methods and the experimental structure.
  2. bF l (%) is the F-score of each method for the ligand protein on the data set.
  3. cF r (%) is the F-score of each method for the receptor protein on the data set.