The PRUNE server takes three files as input, (i) receptor coordinates 
(receptor.pdb), (ii) ligand coordinates (ligand.pdb) and (iii) a file with list 
of transformation matrices giving the docking orientation of the ligand with 
respect to the receptor. The receptor and ligand coordinates should be in the 
PDB format, and the transformation matrices need to be in either of the four
formats available from - FTDock, ZDOCK, PatchDock and Gramm-X. Please choose the
appropriate format from the drop down multiple selection box in the submission 
page. The transformation matrices can be obtained by running the docking search 
techniques using respective softwares. For sample submission, we provide the 
input files from FTDock and ZDOCK software.

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FTDock: 

The ftdock subfolder in this folder contains -
Input files for PRUNE server: receptor.pdb, ligand.pdb and ftdock_global.dat
Output file of PRUNE server: Pruned_trans_matrix.txt 

To submit a sample run in the PRUNE server upload receptor.pdb as receptor file,
ligand.pdb as ligand file, and ftdock_global.dat as Transformation matrix and
select the docking search technique as "FTDock".

Submit the job. The server will output file Pruned_trans_matrix.txt - a file  
with same format as ftdock_global.dat, but, with less number of (pruned)
docking decoys. At the result page, the output file is linked at 
"Pruned Transformation Matrix".

If you wish to generate the ftdock_global.dat file yourself for submission, then
download the FTDock module in your system from
http://www.sbg.bio.ic.ac.uk/docking/download.html and install it.
First preprocess the proteins (receptor.pdb and ligand.pdb) using perl script 
preprocess-pdb.perl and then dock them using ftdock program.

The default output filename of FTDock is ftdock_global.dat with information of 10,000
(default) docking decoys. The tutorial file to run ftdock can be found here
(http://www.sbg.bio.ic.ac.uk/docking/downloads/3d-dock-manual.pdf).

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ZDOCK: 

The zdock subfolder in this folder contains -
Input files for PRUNE server: receptor.pdb, ligand.pdb and zdock.out
Output file of PRUNE server: Pruned_trans_matrix.txt

To submit a sample run in the PRUNE server please upload receptor.pdb as 
receptor file, ligand.pdb as ligand file, zdock.out as Transformation matrix and
select the docking search technique as "ZDOCK".

Submit the job. The server will output file Pruned_trans_matrix.txt.
 At the result page, the output file is linked at "Pruned Transformation Matrix".

If you wish to generate the zdock.out yourself for submission, then
please download the ZDOCK software from http://zdock.bu.edu/software.php
and install it in your system.
To dock two protein molecules viz, receptor.ent and ligand.ent you have to
preprocess PDB file first and then you have to dock them. The commands for
doing that are -

mark_sur receptor.ent receptor.pdb
mark_sur ligand.ent ligand.pdb
zdock -R receptor.pdb -L ligand.pdb -N 10000 -o zdock.out

where zdock.out is the output of the zdock program. The -N option asks for 
10,000 docking decoys. The default output of zdock is 2,000 docking decoys.

The output of the ZDOCK program (zdock.out) can also be obtained by uploading
receptor.ent and ligand.ent to ZDOCK server (http://zdock.bu.edu/),
which provides only 2,000 docking decoys by default and is therefore not
suggested.

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NO SAMPLE SUBMISSION IS PROVIDED FOR PATCHDOCK AND GRAMM-X, BUT YOU CAN
USE THE PROCEDURE BELOW TO GET THE FILE WITH TRANSFORMATION MATRICES.

PatchDock: 
PatchDock transformation matrices file can be obtained by docking two 
protein molecules (receptor.pdb and ligand.pdb) using PatchDock server 
(http://bioinfo3d.cs.tau.ac.il/PatchDock/) or done in your system locally by
downloading and installing the PatchDock software available from
http://bioinfo3d.cs.tau.ac.il/PatchDock/patchdock.html.

Gramm-X: 
GrammX transformation matrices file can be obtained by docking two protein 
molecules (receptor.pdb and ligand.pdb) using GrammX server
(http://vakser.bioinformatics.ku.edu/resources/gramm/grammx/) or 
done in your system locally by downloading and installing the software from
http://vakser.bioinformatics.ku.edu/resources/gramm/grammx/

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The pruned decoys can be scored using PROBE server. At the result page of
PRUNE a button is provided to transfer the control to PROBE server for
scoring. To prevent multiple submission of scoring job, once you submit the
job for scoring, the PRUNE result page will automatically be deleted. So, we
advice to download the receptor, ligand and Pruned_trans_matrix.txt for
your future use before you submit any job for scoring.