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Target Database
Submit Docking
Command Line Access

You might be unable to find PDB native structures but only S3DB prepared structures, via a search by PDB ID or protein name. This is due to the current instability of the API of the Protein Databank. In the meantime, you can search protein structural files directly on the PDB web site, and upload the selected ones on SwissDock. We are sorry for the inconvenience.

Target selection

Ligand selection



Prediction of native binding modes (NBM)

Assay NBM ranked first NBM within the top 5
Native docking 55 % 64 %
Cross docking 26 % 44 %

Using predicted binding modes

Once your job is terminated, you will receive an e-mail with a link to a reference complex and predicted binding modes. They can be converted to your favorite format, or used directly. The ViewDock plugin of UCSF Chimera is very convenient to explore the predicted binding modes.

For experimented users, CHARMM PSF/CRD/RTF/PAR files are also provided for subsequent calculations.

Docking of GDP in GNAQ_HUMAN, a therapeutic target in oncology. The predicted binding mode (magenta/sticks) is superimposed to the X-ray binding mode (ball and sticks) (download the chimera session ).

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