This folder contains the example run files. 
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For Full docking:

Input files: receptor.mmol and ligand.mmol (in PDB format)
Output files: PROBEresult.txt, PComplex_<1 .. 10>.pdb

The input files (receptor.mmol and ligand.mmol) contain only 
protein related coordinates. Water and other small solvent molecules are 
normally removed. Of the two input files, the receptor.mmol is generally of 
the larger size.

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For scoring and ranking:

The example files for scoring and ranking is at scoring folder.

Input files: receptor.mmol, ligand.mmol (in PDB format) and zdock.out
transformation file.
Output files: PROBEresult.txt, struct/PComplex_<1 .. 76>.pdb

The inputs files are protein coordinate files and transformation matrices
required to generate the docking poses. 

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For Full Docking:

For sample submission upload receptor.mmol as receptor file and ligand.mmol as
ligand file. 

Use default rotation (12 degree) and check (by default it is set) the option
to convert MSE to MET. 

Keep the default value (10) of number of predicted complex.

Submit the job.

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For Scoring and Ranking:

For sample submission upload receptor.mmol as receptor file and ligand.mmol as 
and zdock.out as transformation matrix file.

Select the docking search technique as ZDOCK.

Submit the job.

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After successful completion of job, user can download 10 predicted structures
PComplex_<1 .. 10>.pdb along with all the score information of 10 complexes in
ProbeResult.txt. Receptor and ligand files can also be downloaded from the
result page.