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Test Sets
WARNING: These test sets are designed for validation and comparison purposes ONLY, and thus should only be downloaded by experienced users. If you are new to DOCK, please see our tutorials for descriptions of how to work various portions of the program.
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SB2012 Docking Database
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Protein Binding Mode Test Set
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Description:
Set of 114 crystallographically determined protein-ligand structures. Files and scripts for preparing complexes for docking are included. Optimized parameters for rigid and flexible ligand binding pose prediction are also included.
Results:
RMSD from crystal structure and DOCK Score for each member of the group use optimized parameters. Highlighted items were considered successesful recreation of binding poses.
Reference:
Moustakas DT, Lang PT, Pegg S, Pettersen EF, Kuntz ID, Broojimans N, Rizzo RC. Development and validation of a modular, extensible docking program: DOCK 5. Submitted.
Parallel Processing Test Set
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Description:
The two libraries of small molecules, one containing 500 and the other 1000 small molecules, were filtered to have less than 5 and less than14 rotatable bonds, respectively. The receptor used as a target for this study was HIV-1 reverse transcriptase in complex with nevirapine (pdb code 1VRT). Nevirapine was flexibly redocked using the optimized parameters, which yielded a ligand orientation 0.28 Å RMSD from the crystal structure orientation. In addition, a library consisting of 1000 copies of neviripine was generated to remove dependence on the order and size of the compound library.
Results:
Length of calculation graphed against number of processors used for all three libraries.
Graph (pdf)
Reference:
Moustakas DT, Lang PT, Pegg S, Pettersen EF, Kuntz ID, Broojimans N, Rizzo RC. Development and validation of a modular, extensible docking program: DOCK 5. Submitted.
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