ZDOCK Tutorial


ZDOCK Tutorial

ZDOCK is a rigid protein docking program based on Fast Fourier Transform, created by the University of Massachusetts Medical School. ZDOCK will search all translation and rotation spaces of the two proteins, and then score each possible pose. The scoring function is an energy-based scoring function, which calculates potential energy, spatial complementarity, and electric field force.


(1) Enter the website


The interface is very simple. Two input proteins, the first input protein will stand still during the docking, and usually put a larger protein on it. The second input protein will move and rotate during the docking, and usually put a relatively small protein.

Enter your email, the id number of your job and the result will be sent to your mailbox, tand the rest remain unchanged.

ZDOCK Tutorial

(2) Use calculation examples

Click directly on the input of example1 at the bottom.

The following interface appears. There are two modes for protein input, one is to upload the local PDB file, and the other is to directly enter the PDB id number.

ZDOCK Tutorial

(3) Select binding residues and block residues

Click the submit button

The selection of binding residues means that the residues that may be bound are known in advance, the so-called key residues.

The block residue means a residue site that is known to have no effect on binding.

Through the choice of the above two, the docking range can be effectively reduced and the required conformation can be produced.

No residue selection is made this time.

The yellow part represents the visual interface of the protein (in fact, it is not very useful).

ZDOCK Tutorial

(4) Waiting for the result

After the selection is complete, click the submit button, and select ok in the next interface, until this interface appears at the end, check your mailbox, and wait for the result.

ZDOCK Tutorial

(5) Download the results

Enter directly, the second email, click the link to enter the download interface.

There are four options in Download Files:

ZDOCK Output: Contains configuration and scoring information, starting from row 6, the last column is scoring, and the red box is marked

Receptor PDB: Imported receptor protein file

Ligand PDB: Imported ligand protein file

Top 10 Predictions: the top 10 poses

Click Top 10 Prediction to download the result, unzip the file, and view it with visualization software, Pymol, Chimera, VMD, etc.


The biological function of protein is mainly through the interaction of the specific part of its binding surface with other small molecules or biological macromolecules. Predicting possible binding sites on the surface of protein molecules through computational methods is conducive to computer-aided drug design based on protein structure, and further promotes the process of new drug development.

* For Research Use Only.
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