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Table 5 Results of the redocking experiments performed on the PPDbench dataset

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

PDB IDDoFsatomsVinaDINCPDB IDDoFsatomsVinaDINC
2HO213717.58 ±1.302.64 ±0.414B4N401108.82 ±0.955.21 ±0.61
2O9V15696.07 ±0.291.98 ±0.773AWR41848.25 ±0.744.94 ±0.37
3OBQ19627.50 ±0.702.52 ±0.932PEH41887.13 ±1.104.54 ±0.15
1CKA22656.78 ±0.182.68 ±0.492XVC419910.67 ±1.562.53 ±0.35
2A25236010.65 ±1.541.45 ±0.983GYT42817.14 ±0.475.63 ±0.30
2R9Q24595.93 ±0.722.25 ±0.221H6W428511.13 ±2.142.65 ±1.68
4H4F25723.75 ±0.201.05 ±0.032O4J42878.18 ±0.954.82 ±0.56
1SSH25768.31 ±1.045.04 ±0.304GQ642996.98 ±1.364.65 ±0.28
3TJV26635.45 ±1.781.43 ±0.052XRW421009.19 ±1.246.26 ±0.67
3ERY27706.26 ±1.553.10 ±0.383DS4421037.85 ±0.824.79 ±0.36
3I5R27705.71 ±0.243.67 ±0.632PUY43808.94 ±2.463.94 ±0.30
1MFG29717.27 ±1.783.88 ±0.132P1T43865.86 ±1.094.05 ±0.74
1YWO29806.89 ±1.663.50 ±0.231D4T449014.65 ±1.084.81 ±0.87
1QKZ30625.63 ±1.712.82 ±0.392QSE45897.21 ±0.685.25 ±0.23
1K5N30644.66 ±0.992.84 ±0.631RXZ45977.35 ±0.813.53 ±0.91
1OAI30667.75 ±0.283.03 ±0.432BBA451157.18 ±0.825.08 ±0.35
1U0030717.01 ±1.082.20 ±0.151NQ746908.06 ±0.415.46 ±0.30
1RST30767.16 ±0.364.37 ±0.143KMR46907.02 ±0.865.36 ±0.36
4GXL30817.41 ±1.012.69 ±0.203VTC46918.59 ±0.915.63 ±0.11
3RM131716.23 ±0.883.21 ±0.632P5446977.40 ±0.755.14 ±0.34
2D0N32709.69 ±2.483.56 ±0.542QOS46977.64 ±0.375.89 ±0.33
2VR3327112.06 ±2.676.30 ±1.433RQG47927.09 ±0.295.34 ±0.24
4HTP32859.02 ±0.274.52 ±0.884ERY471007.19 ±0.333.61 ±0.59
2CE833707.19 ±0.354.59 ±0.662FTS471048.04 ±0.424.54 ±0.24
4F1Z337215.69 ±2.992.88 ±0.171OW648949.95 ±0.527.23 ±0.39
2ZJD33772.77 ±0.531.79 ±0.073C3R481048.94 ±1.475.87 ±0.34
3W1B33859.93 ±0.525.21 ±1.193L0E49987.08 ±1.095.22 ±0.10
3V2X348410.65 ±0.962.56 ±0.463OLF49996.51 ±0.575.49 ±0.27
3PTL357110.92 ±2.823.99 ±0.191T08491158.98 ±0.815.36 ±0.97
1X2R35746.51 ±0.954.12 ±0.401NLN50947.41 ±0.882.96 ±0.85
3KUS35837.28 ±1.992.53 ±0.574J8S501026.63 ±0.614.79 ±0.18
3U9Q36695.64 ±1.243.34 ±0.352FMF501079.26 ±0.856.54 ±0.33
1T7R36775.21 ±0.303.15 ±0.472FFF501097.98 ±0.524.72 ±0.77
2QBX36804.02 ±0.802.47 ±0.563QIS501095.91 ±0.443.85 ±0.49
1NX136815.57 ±0.654.01 ±0.472PUX501119.27 ±1.715.18 ±0.28
2W2U36916.17 ±1.493.49 ±0.492CCH511028.26 ±0.454.94 ±0.81
1UJ037747.02 ±1.103.89 ±0.402WHX511098.41 ±0.694.98 ±0.72
2HT937857.72 ±0.755.74 ±0.232VWF511158.28 ±1.555.65 ±0.22
1EG4371068.97 ±0.864.64 ±0.262B9H521019.73 ±2.174.53 ±0.53
2FVJ38816.83 ±0.445.13 ±0.243UP3531088.75 ±0.836.28 ±0.19
3LL838853.70 ±1.011.98 ±0.153H1Z531369.89 ±2.025.04 ±0.33
1T4F38867.52 ±0.815.27 ±0.131PZL551147.79 ±0.625.62 ±0.31
1TFC39817.02 ±0.644.95 ±0.284K0U621308.31 ±0.745.90 ±0.49
2DYP39813.70 ±0.911.71 ±0.122V8Y671299.10 ±1.426.09 ±0.36
1NTV39896.20 ±0.873.27 ±0.69average7.7 ±1.014.17 ±0.45
  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 and DINC using their defaults parameters