LZerD

Multi-LZerD: Multiple protein docking for asymmetric complexes

About 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 uses 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.

Copyright

Copyright of this distribution belongs to Juan Esquivel-Rodríguez, David Yang & Daisuke Kihara. It's free for academic non-profit institutions. For commercial entities or government research labs, please contact us (dkihara@purdue.edu) to get the approval to use this distribution. Redistribution of any files in this pack without our allowance is prohibited.

Download Multi-LZerD

The current version of Multi-LZerD is available as a tar.gz file and can be downloaded here. Execution instructions are given in the README file provided.

LZerD: Protein-protein Docking Algorithm

About LZerD

The program LZerD (Local 3D Zerike descriptor-based Docking algorithm) uses geometric hashing to generate ligand orientations using the 3D Zernike descriptor as the shape matching criteria. Scoring is based on a 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.

Implementation details are available from the paper Protein-protein docking using region-based 3D Zernike descriptors, Vishwesh Venkatraman, Yifeng D Yang, Lee Sael and Daisuke Kihara, BMC Bioinformatics, 10: 407, (2009)

Copyright

Copyright of this distribution belongs to Vishwesh Venkatraman, Sael Lee, David Yang & Daisuke Kihara. It's free for academic non-profit institutions. For commercial entities or government research labs, please contact us (dkihara@purdue.edu) to get the approval to use this distribution. Redistribution of any files in this pack without our allowance is prohibited.

Download LZerD

The current version of LZerD as used in the paper is available as a tar.gz file and can be downloaded here. The archive contains the following files

LZerD1.0 - The docking program
mark_sur - marks surface atoms
uniCHARMM - file required by mark_sur
GETPOINTS - for generating points on the molecular surface
LZD32 - generates the 3D Zernike invariants for points on the surface
points, SASA.rc - file required for the Solvent accessible surface area calculation
PDBGEN - Given the set of predictions output by LZerD, this program sorts them by the score (highest to lowest( and generates PDB files for the top k=3 orientations of the ligand. The value k can be modified by the user.
runlzerd.sh - A shell script which when provided with ligand and receptor pdb files runs all the above mentioned programs in sequence and generates the required output
README - A file with instructrions for usage
example - A directory with sample output from a LZerD run on 1PPE (1PPE_l_b, 1PPE_r_b). 1PPE_l_b.pdb, 1PPE_r_b.pdb - original PDB files provided by the user
1PPE_l_b.pdb.ms, 1PPE_r_b.pdb.ms - PDB files with surface atoms marked by mark_sur
1PPE_l_b.gts, 1PPE_r_b.gts - molecular surface for ligand and receptor produced by GETPOINTS
1PPE_l_b_cp.txt, 1PPE_r_b_cp.txt - Sparse point representation of the ligand and receptor surface produced by GETPOINTS
1PPE_l_b_01.inv, 1PPE_r_b.inv - Zernike invariants for selected points on the surface produced by LZD32
1PPE_r_b_1PPE_l_b.out - Transformation file with scores generated by LZerD1.0
1PPE_b.stat - Interface RMSDs (Root Mean Square deviations) and scores for each orientation
ligand1.pdb, ligand2.pdb, ligand3.pdb - The 3 top ranked predictions

HARDWARE REQUIREMENTS

This distribution includes exectutable 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.

UNPACKING

To unpack the distribution execute the following commands on the console

gunzip lzerddistribution.tar.gz
tar -xvf lzerddistribution.tar

This will generate the directory "lzerddistribution" with the contents as listed above.

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 format of the output is shown below. The first line 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.

LIG: 0.926583 0.541623 2.32135 -1.96904 -8.93765 -2.37821
0.174 -0.868 -0.465 -0.948 -0.275 0.160 -0.267 0.413 -0.871 37.305 5.810 -2.871 397.116
0.943 0.331 0.021 -0.328 0.923 0.200 0.047 -0.196 0.980 -0.926 14.748 0.331 496.970
0.969 0.028 0.247 -0.150 0.859 0.490 -0.198 -0.511 0.836 1.002 10.327 -0.061 370.243
... ... ... ... ... ... ... ... ... ... ... ... ... ... ###.##
... ... ... ... ... ... ... ... ... ... ... ... ... ... ###.##

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