#LZerD
The program LZerD uses geometric hashing to generate ligand orientations using the 3D Zernike
descriptor as the shape matching criteria. Scoring is based on as shape complementarity term
defined by the local shape Zernike and orientation of the surface normals. In addition a
clash penalty term and buried surface area have also been incorporated.

#DETAILS
This distribution includes executable files for LZerD1.0 and other utilities required by the program.
(GETPOINTS, LZD32, mark_sur, points, SASA.rc, PDBGEN, runLZerD.sh, example). All files have been compiled on a 
GenuineIntel Pentium 4 processor(http://www.intel.com/products/processor/pentium4/) running on a 
LINUX (Ubuntu 8.04.2) operating system. The current version of LZerD requires around 1.5GB RAM, so please ensure 
that the system has sufficient memory resources. Docking times range between 1.5 to 6 hours depending on 
the size of the protein and the number of surface points considered. 

NOTE: The program has only been tested on machines running LINUX.

#USAGE
To run the program please use the "runlzerd.sh" script by providing it with two pdb files i.e.
the receptor and ligand.
Parameters for the run have been preset.
At the end of the docking run, the program outputs the top 3 orientations as judged by the LZerD score.
An example has been provided for the protein 1PPE in the "example" directory.

Example:
./runlzerd.sh 1PPE_r_b.pdb 1PPE_l_b.pdb
ATTENTION: Both ligand and receptor PDB files must be in the "lzerddistribution"  directory i.e.
in the same directory as the executables.
It is advised to copy the proteins to be docked into the "lzerddistribution" folder and then run the 
script as shown above.
Users may need to make the shell script executable and this can be done by executing the command
"chmod +x runlzerd.sh" on the console.

#OUTPUT
The first line of the output is the translation and random rotation applied to the ligand.
The transformations are output as a set of 12 numbers, the first 9 forming the 3 rows of a
rotation matrix and the other 3, the translation to be applied after rotation. The last column
is the score for the given orientation. Solutions are ranked based on the score from highest to lowest.

#UPDATE
2014-12-12, updated "LZD32". fixed "NaN" and "inf" bugs.
2016-11-02, updated "PDBGEN". fixed hydrogen bug.
            updated "GETPOINTS". fixed non-deterministic output.
            added "LB3Dclust" to cluster a list of ligand*.pdb files output by PDBGEN.

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