Supplementary material for the DockRank journal paper

 

Please note that this paper used the docked models generated by Cluspro 2.0 using the Balanced energy function.

Cluspro2-BM3 decoy set:

The PDB files of docked models

The mapping between Cluspro task IDs and case IDs

The L-RMSD of docked models

Cluspro Energy Scores

DockRank Scores on the ClusPro2-BM3 decoy set

Some notes about this decoy set:

1. Two of the docked models returned by ClusPro 2.0 are abnormal. Several lines of PDB files are combined into one line.

      Dataset: Docking Benchmark 3.0

      Case ID: 1KTZ

      model ID: model.000.10

      ClusPro job ID: 6977

      Dataset: Docking Benchmark 3.0

      Case ID: 1CGI

      model ID: model.002.10

      ClusPro job ID: 6902

2. We found for two cases, 1RLB and 1ML0, one of the two ligands were left out by the authors of the BM3 dataset. Each of the case should have two identical bound ligands, however, the original BM3 set only include the coordinates of one ligand as bound ligand, which may cause docked models near the other bound ligand position regarded as wrong models. Here we attach the bound PDB files for case 1RLB and 1ML0. We also recalculated the L-RMSD for all the docked models by including both of the two identical bound ligands. The smaller value of L-RMSDs between a docked ligand and two bound ligands is used as final L-RMSD for this model.

1RLB

1ML0

DockRank scores on other decoy sets:

ZDock3-BM3 decoy set

CAPRI uploader models for Targets 35, 36, 41, 47 and 50

Note:

ZDock3-BM3 decoy set can be downloaded from ZDock website. 54,000 decoys per case.

CAPRI uploader set are not publicly available.

The last column of the csv file is the DockRank score for each decoy. The higher the score, the higher the decoy is ranked. For example, the decoy with the highest DockRank score will be ranked as top 1 model.