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Table 1 Results of the redocking experiments performed on the Dhanik dataset

From: Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins

PDB IDDoFsatomsVinaVina10012 ×Vina24 ×VinaDINC288 ×VinaDINC best
2FZC7183.51 ±0.453.54 ±0.202.80 ±0.312.77 ±0.242.76 ±0.242.242.24
1TYR8225.17 ±1.664.17 ±1.732.77 ±0.162.35 ±0.281.82 ±0.261.811.62
1V2O10303.53 ±0.073.27 ±0.222.65 ±0.232.58 ±0.192.39 ±0.182.172.17
2DRC10337.19 ±0.397.69 ±0.643.51 ±2.693.30 ±2.561.06 ±0.181.000.97
1NWL11315.31 ±1.085.19 ±1.823.03 ±0.612.23 ±0.501.49 ±0.111.611.18
1ELB13334.56 ±0.134.48 ±0.033.35 ±0.582.72 ±0.572.18 ±0.282.201.90
3GSS18395.29 ±1.094.96 ±0.703.15 ±1.122.73 ±0.973.10 ±0.201.741.61
1IS018475.90 ±1.343.37 ±0.803.44 ±0.552.20 ±0.712.20 ±0.331.361.32
1A1B19393.03 ±0.283.18 ±0.472.40 ±0.401.97 ±0.531.97 ±0.411.271.27
1JQ920477.99 ±2.209.51 ±0.215.41 ±1.395.48 ±1.772.90 ±0.152.462.46
4FIV20582.77 ±1.281.11 ±0.500.79 ±0.360.60 ±0.030.62 ±0.090.550.49
4ER222483.42 ±0.452.40 ±0.752.30 ±0.601.98 ±0.491.55 ±0.091.351.33
1G7Q22573.99 ±1.352.01 ±1.152.23 ±1.011.48 ±0.201.10 ±0.071.110.98
1SLG23597.30 ±1.796.43 ±2.173.76 ±1.423.13 ±1.012.36 ±0.102.131.91
1FZK23686.64 ±0.723.94 ±1.844.26 ±1.761.94 ±0.621.20 ±0.151.371.11
2ER925652.87 ±0.392.67 ±0.292.09 ±0.212.10 ±0.341.87 ±0.111.521.52
1FKN29634.67 ±1.273.56 ±0.383.08 ±0.142.83 ±0.222.11 ±0.282.081.75
1PZ529675.54 ±0.816.28 ±0.104.69 ±0.734.49 ±0.223.16 ±0.293.901.87
1FO030707.36 ±1.224.78 ±1.083.29 ±1.832.92 ±1.571.05 ±0.191.040.73
average5.05 ±0.954.35 ±0.793.11 ±0.852.62 ±0.691.94 ±0.201.731.50
  1. For each complex in the dataset, we first list its identifier in the protein data bank (PDB ID), its number of rotatable bonds, i.e., degrees of freedom (DoFs), and its number of heavy atoms. Then, we list the average all-atom RMSD (over five replicates) associated with the top-RMSD conformation produced by Vina, Vina100, 12 ×Vina, 24 ×Vina, and DINC (see the “Results” section for explanations on these docking protocols), as well as the standard deviation. Finally, we list the all-atom RMSD associated with the top-RMSD conformation produced by 288 ×Vina and DINC best