ZDOCK

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The Basics
Submitting Jobs
Job Output
FAQ

The Basics

ZDOCK and M-ZDOCK

ZDOCK and M-ZDOCK are Fast Fourier Transform based protein docking programs authored and maintained by Zhiping Weng's lab (ZLAB) at the University of Massachusetts Medical School.

ZDOCK searches all possible binding modes in the translational and rotational space between the two proteins and evaluates each pose using an energy-based scoring function.

M-ZDOCK is an adaptation of ZDOCK to predict the structures of cyclically symmetric multimers, based on the structure of a protein.

More details on ZDOCK and M-ZDOCK can be found in the references.

Scoring Functions

Two ZDOCK versions are available for use on the server, with scoring functions consisting of these terms:

ZDOCK 3.0.2's scoring function is shown to have superior predictive performance versus ZDOCK 2.3.2 using an unbound protein docking benchmark of 176 test cases. The server also has an option for the older output format if desired for post-processing ("ZDOCK 3.0.2f", "ZDOCK 2.3.2f") which gives a slower running time, but no change in predictive performance.

M-ZDOCK currently uses the ZDOCK 2.3.2 scoring function.

Blocking, Filtering and Output

After specifying PDB files for docking, the user can specify residues for blocking from the binding site during docking (ZDOCK and M-ZDOCK), and select binding site residues for filtering output predictions (ZDOCK only) using an interactive JMol-enabled interface.

Output from the server includes ZDOCK or M-ZDOCK output file, processed PDBs (for generating predicted models), and interactive tools to view and generate individual predictions or sets of predictions.

Contact

For questions, please contact the ZDOCK Server Team: zdock@umassmed.edu.


Submitting Jobs

Input PDB Files

ZDOCK and M-ZDOCK require PDB files as input. Users can provide their own PDB file, or enter a PDB ID to select a biological assembly or chain(s) directly from the PDB. An image of the biological assembly is provided upon entering a PDB code.

For ZDOCK jobs, Protein 1 will be stationary in the output predictions while Protein 2 will be moved, so it may be of interest to submit the larger or receptor protein as Protein 1.

Email Address

The ZDOCK Server will send a link to the docking results (as well as a confirmation email upon job submission) to the email address you enter. Due to ZDOCK and M-ZDOCK licensing, only academic or non-profit email addresses are allowed. If you are a commercial user, please contact support-us@accelrys.com and ask about ZDOCKpro.

Other Submission Options

Skip residue selection

When checked, the selection of blocking and contacting residues will be skipped and the job will be submitted directly upon clicking the "Submit" button.

Select ZDOCK version (ZDOCK only)

As noted above, users have the option of specifying the latest version of ZDOCK ("ZDOCK 3.0.2"; default), the previous version ZDOCK ("ZDOCK 2.3.2"), as well as these two versions with the older output format if desired for post processing ("ZDOCK 3.0.2f", "ZDOCK 2.3.2f").

Select Symmetry (M-ZDOCK only)

Users can select whether to predict dimeric, trimeric, or higher order assemblies using M-ZDOCK

Blocking Residues

ZDOCK and M-ZDOCK can block specific residues from being in the binding site via an interactive page (please allow Java to load to permit the JMol visualization of the protein(s)). Any number of residues can be selected from the scrolling list; selected residues will appear as red sticks on the corresponding structure. To select multiple residues use the shift key (consecutive selections) or control key (non-consecutive selections) in combination with the mouse. To deselect residues, use the control key in combination with the mouse.

More Details: The ZDOCK server gives an atom type of 19 to all atoms in residues selected for blocking, which is a dummy atom type with strongly unfavorable ACE or IFACE contact energy. This significantly lowers the chance of that residue being in the predicted binding site.

Contacting Residues (ZDOCK only)

ZDOCK will filter results such that only those with specified residues in the binding site are returned. Any number of residues can be selected from the scrolling list; selected residues will appear as blue sticks on the corresponding structure. To select multiple residues use the shift key (consecutive selections) or control key (non-consecutive selections) in combination with the mouse. To deselect residues, 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 your filtered output had all predictions removed (as noted on the Results page) or too few predictions are in your output, you may want to reduce the number of residues selected for Contacting Residues as this restricts the predictions in the ZDOCK result file.


Job Output

Results Page

When jobs are completed on the server, an email will be sent notifying the user of job completion along with a link to the results page. The results page features:

For ZDOCK output, if contacting residues were specified by the user, a message at the top of the results page will note the number of predictions removed from the output file due to contact filtering. If all predictions were removed (no predictions contained all contacts specified by the user), this will be noted, and the unfiltered ZDOCK output will be provided for reference.

Creating Predicted Complexes

In addition to the top 10 predictions and the means to download other individual predictions directly from the results page, users who wish to generate larger sets of predicted complexes have two options: a Java program, and a command-line program. The Java program has a GUI interface and is recommended; more advanced users and those without Java may prefer to use the command-line interface. For both programs, users must first download the docking output file and input PDB file(s) from the results page to their computer.

Java Program

Step 1: Launch the Java program for ZDOCK or M-ZDOCK. The jnlp (Java Web Start) program may download to your machine; if so, double click on it when the download is complete to start it.

Step 2: Select the ZDOCK or M-ZDOCK output file on your local machine, choose the range of prediction numbers you wish to generate, and click the "Create" button. The prediction files will automatically be generated in the zdock output file's directory. Prediction files are named complex.X.pdb where X is the ranked prediction number. For example, "complex.1.pdb" is the top ranked prediction.

Command Line: ZDOCK

Step 1: Download and decompress the tar file of ZDOCK 3.0.2 or ZDOCK 2.3.2 that is appropriate for your platform. Tar files can be found here.

Step 2: Copy the create_lig program to the directory with the zdock output file.

Step 3: Run the script "create.pl" from this directory. "create.pl [zdock_output_filename]" will generate ALL predicted complexes in the zdock output file and name them "complex.X" where "X" is the prediction number. To create the top N prediction files, just truncate the zdock output file. This can be accomplished in unix by "head -N [zdock_output_filename] > [zdock_output_short]" where N is the number of predictions plus number of header lines in the output file (5 by default, 4 if 3.0.2f or 2.3.2f was selected for ZDOCK version). Then run create.pl with the new file as input.

Command Line: M-ZDOCK

Step 1: Download and decompress the tar file of M-ZDOCK that is appropriate for your platform. Tar files can be found here.

Step 2: Run the "create_multimer" program in the directory with your M-ZDOCK output file and input PDB file to generate ALL predictions from M-ZDOCK. To generate a subset of the top N predictions, make a dummy output file with the top N+3 lines, e.g. "head -13 mzdock.out > mzdock.dummy.out", then run create_multimer using mzdock.dummy.out, to get the top 10 predictions from file "mzdock.out". Alternatively the "create_multimer_num" program can be used to generate individual predictions from the command line.


FAQ

Q: My output PDB files from ZDOCK do not display well in a viewer, or I can't see both molecules. What can I do?
A: We would suggest checking the chain IDs of the two PDB files you used, and if there are redundant chain IDs (e.g. fileA contains chain A and fileB contains chain A), this may confuse the molecular viewer and make it difficult to highlight molecules according to chain (ZDOCK does not alter chain IDs to generate PDB files of predicted complexes). We would suggest re-naming redundant chains prior to submitting to the server, or if the job is completed you can modify the PDB file prior to generating predictions using the Java or command line programs.

Q: Why are there very few predictions in my ZDOCK output file? Why is there a message saying that all predictions were removed from the ZDOCK output file?
A: Predictions were removed by filtering if they do not contain ALL residues specified by "Contacting Residues" in the predicted interface. Select fewer residues as contacting residues.

Q: What are the columns or fields in the ZDOCK output file?
A: Please see this page.