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Introduction:

ZDOCK is a Fast Fourier Transform based protein docking program. It takes two PDB files and outputs the predicted structure of their complex. The top 2000 ranked predictions are returned.

How ZDOCK Works:

ZDOCK searches all possible binding modes in the translational and rotational space between the two proteins and evaluates each by an energy scoring function. Search speed is greatly increased by converting each protein's structure to a digital signal and utilizing a Fast Fourier Transform technique to reduce computational time. The specific details of ZDOCK can be found in the following papers.

Uploading Files:

ZDOCK requires two PDB files as input. Users can no longer use the "Upload file" field to enter in the PDB Code of a structure that does not reside on their machine. Unfortunately, the new versions of the Firefox and Internet Explorer browsers have disabled passing text through the file field. We regret that this means we'll now have to require the user to upload the PDB file directly.

Blocking Residues:

ZDOCK can block specific residues from being in the binding site. Any number of residues can be selected in the scrolling list. To select multiple residues use the shift key (consecutive selections) or control key (non-consecutive selections) in combination with the mouse. To deselect residues also use the control key in combination with the mouse.

More Details: ZDOCK applies an ACE type of 0 to all atoms in residues selected for blocking. The result is an unfavorable desolvation energy contribution that significantly lowers the likelihood of that residue being in the binding site.

Contacting Residues:

ZDOCK will filter results such that only those with specified residues in the binding site are returned. Any number of residues can be selected in the scrolling list. To select multiple residues use the shift key (consecutive selections) or control key (non-consecutive selections) in combination with the mouse. To deselect residues also use the control key in combination with the mouse.

Results from the top 2000 ZDOCK predictions are filtered using the user-defined residues and a 6 angstrom distance cutoff. Predictions are only kept if ALL residues selected are within 6 angstroms of the partner protein

Note: If you do not see any predictions in your output file (just the four header lines) or too few predictions than preferred, you should reduce the number of residues selected for Contacting as this restricts the predictions in the ZDOCK result file.

Residue Selection by Distance:

For Blocking

Distances can be used to define a residue selection. Each residue picked can then be assigned a distance cutoff which determines the radius of the selection around that residue. All distances are in angstroms. All residues in the selection list define an area on the protein in which docking is scored unfavorably as explained in Blocking Residues

The "Restrict Selection to Surface Residues Only" option restricts your selection to only surface residues, allowing only residues that are on the surface and within the distance cutoff from being included in the selection. This option is recommended for blocking residue selections because core residues make very little contribution to the overall docking score and therefore will not make a significant effect on blocking selections.

For Contacting

Distances can be used to define a residue selection. Each residue picked can then be assigned a distance cutoff which determines the radius of the selection around that residue. All distances are in angstroms. All residues in the selection list are then used to filter the prediction set as explained in Contacting Residues

The "Restrict Selection to Surface Residues Only" option restricts your selection to only surface residues, allowing only residues that are on the surface and within the distance cutoff from being included in the selection. Using this option in contacting residue selections is highly recommended because core residues will always be farther away from the partner protein than the surface residues

Creating Predicted Complexes:

Creation of the ZDOCK predicted complexes can be done automatically on the web through a Java program or offline by running a Perl script. Automatic complex generation is highly recommended. However, due to security concerns in the Java program that arise by creating files on your local machine directly from the web, you may wish to generate them manually. Please also bear in mind that we do not change the chain ID of the original files submitted, so if your receptor and ligand have the same chain ID, the resulting complex file will consist of only one chain ID.

Automatically

Step 1: Download the zdock output file, the receptor file, and ligand file which were supplied in your job completion email. Then click here to launch the java program.

Manually

Step 1: Create a directory on your computer, and download the zdock output, receptor and ligand file to this directory.

Email Address:

ZDOCK Server will send your docking results to the email address you submitted. Due to licensing, only academic or non-profit email addresses are allowed. If you are a commercial user and wish to use ZDOCK, please contact www.3ds.com/how-to-buy and ask about BIOVIA Discovery Studio and ZDOCK.