#Multi-LZerD
Multi-LZerD is a generic multiple protein docking program that can create
docking models without additional biological information (like symmetry constraints).
It is based on LZerD which usees geometric hashing and the 3D Zernike descriptor
for pairwise docking purposes.
Based on the pairwise predictions, Multi-LZerD applies a Genetic Algorithm to combine
2-body transformations in order to create a complete protein complex from the original parts.
It uses a physics based score to guide the GA towards the best solution possible.

#DETAILS
This distribution includes files required to run LZerD and Multi-LZerD. A script that
triggers the main process (run.sh) along with a sample set of PDB files. The man script
can be modified easily in order to obtain predictions for new complexes.

The program provided has been tested on Linux platform only (Ubuntu 10.04.1 LTS).

#USAGE
To start the overall process call the run.sh script. By default this script uses A-sample.pdb,
B-sample.pdb and C-sample.pdb as a 3 chain complex example. In general, the program requires that
files follow this type of naming format: <chain id>-<complex name>.pdb.

In order to run Multi-LZerD with your own complex, modify the run.sh script and change the
complex name (basename variable) and a list of the chain ID's that identify the subunits (units variable).

Notes:
-All scripts assume that all files are located in the current directory
-It is possible that script files (.sh and .pl) need to be given execution permissions
	(i.e. using "chmod +x <scriptfile>")

#OUTPUT
A file with ".ga.out" suffix contains the final predictions after the Genetic Algorithm concludes.
PDB files, called decoy*.pdb, that represent those structures are generated. Additionally, refined*.pdb
files represent the refinement of each decoy structure.

#CONTACT
Please report comments and bugs to dkihara@purdue.edu
