Decoy Sets

Below are sets of docking predictions made by various ZDOCK versions on our protein docking Benchmark (version 4.0, 176 test cases). In addition, we've included ZDOCK 3.0.2 and ZDOCK 3.0 predictions (generated using 6 degree sampling) re-ranked by our scoring algorithm IRAD (a new version of ZRANK). You are welcome to use these sets to test your own energy functions and tools (please reference accordingly; see the included README file). Each tar file contains:

• Structure predictions (in ZDOCK output format)
• Evaluations of the predictions (root mean square distance, or RMSD, from the bound interface)
• The benchmark PDB files that were used as docking input
• A program to generate structures of docking predictions from the ZDOCK output.

Decoy sets are available for 6 degree sampling (54000 predictions per test case) and 15 degree sampling (3600 predictions per test case), for several ZDOCK versions.

Predictive performance of ZDOCK and IRAD for these decoy sets is summarized here. Details are included with the decoy set files.

IRAD (formerly ZRANK) - re-ranked ZDOCK predictions

ZDOCK 3.0.2, IRAD
ZDOCK 3.0, IRAD

ZDOCK 3.0.2

ZDOCK 3.0.2, 6 degree sampling
ZDOCK 3.0.2, 15 degree sampling

"Fixed receptor" format, for users requiring the older ZDOCK output format for their programs or scripts:

ZDOCK 3.0.2, 6 degree sampling, fixed receptor
ZDOCK 3.0.2, 15 degree sampling, fixed receptor

ZDOCK 3.0

ZDOCK 3.0, 6 degree sampling
ZDOCK 3.0, 15 degree sampling

ZDOCK 2.3

ZDOCK 2.3, 6 degree sampling
ZDOCK 2.3, 15 degree sampling



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