ZDOCK3.0 Decoys for Benchmark4

This is a README file for the ZDOCK3.0 6 degree sampling decoy set for Benchmark4.
The contents are:
input_pdbs/    :       directory with benchmark PDB files
results/*.fg.out:      structure predictions in ZDOCK output format
results/*.rmsds:       RMSDs of the structure predictions
stats.bm4.zd3.0.fg.txt: RMSD stats of the predictions

To generate the predicted structures, put create.pl, the create_lig executable 
and the PDB files in a directory with the ZDOCK output file. Then execute
create.pl:
./create.pl zdock_output_file [N_preds]
The N_preds argument is optional and will tell create.pl to generate only the
top N_preds predictions. The create_lig executable is compiled on Linux; the source
code and makefile are provided in case of a different platform (type "make" in their
directory to compile). 

The RMSD files are generated by calculating the interface Ca RMSD of each
prediction with respect to the bound structure (each line has a prediction
number and the RMSD separated by tab). The stats files have the test case,
number of hits in top 2000, rank of first hit, and RMSD of first hit on each
line. Each hit is defined as a prediction with Ca RMSD < 2.5 Angstroms. 
Difficult cases are excluded from the stats files as they have no hits using
ZDOCK due to the large conformational change of the unbound structures. The
ZDOCK predictions are nevertheless included in the decoy set in case the user 
wants to work with these predictions. 

More about the Benchmark can be found at this site:
http://zlab.umassmed.edu/benchmark/

To reference ZDOCK and the Benchmark, please cite:

ZDOCK3.0:
Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z (2007).  Integrating Statistical Pair Potentials into Protein Complex Prediction.  Proteins 69(3), 511-520.

Benchmark4.0:
Hwang H, Vreven T, Janin J, Weng Z (2010). Protein-Protein Docking Benchmark Version 4.0. Proteins 78(15), 3111-3114.
