Supplementary material for DockRank ACM-BCB 2011 paper

 

The scatter plot of rankings for the docking cases that can be predicted by PS-HomPPI.pdf

Please note that ACM-BCB 2011 paper used docked models generated by Cluspro 2.0 using Electrostatic-favored energy functions.

Cluspro 2.0 - 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

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