How to view SwissDock result locally on PC?

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Ashok Kamalanathan

SwissDock is a web-based docking program that allows users to predict the binding mode and binding affinity of small ligands to protein targets. The results of SwissDock are typically visualized and analyzed through a web browser, but it is also possible to download the results and view them locally on your PC.

Here are the steps to view SwissDock result locally on your PC:

Go to the SwissDock website (https://www.swissdock.ch/).

Perform a docking simulation by providing the necessary input files (protein and ligand structures in PDB format) and selecting appropriate docking parameters.

Once the simulation is complete, you will be redirected to the results page, where you can view the predicted binding mode and binding affinity of the ligand.

To download the results, click on the "Download" button located on the right-hand side of the page.

Select the "Results in PDBQT format" option and click on the "Download" button.

The downloaded file will be in the PDBQT format, which can be opened and viewed using molecular visualization software such as PyMOL, Chimera, or VMD.

Install any of the molecular visualization software mentioned above, open it, and then open the downloaded PDBQT file.

Once you have opened the file, you can visualize and analyze the docking results locally on your PC.

David L. Murphy

Just an FYI-Those SWISSDOCK output chimeraX files can only be opened/used within 1 week of getting your docking results on the web server, after 1 week the file the won't open/load in the chimera application, so make sure you do your analysis very quickly as soon as you get your results output. I think the web server only holds your docking results on their server for 1 week, the chimeraX file needs to access the stored result on their server to work I think- hope this helps.

Susanta Roy

If you are still encountering difficulties, you can try using alternative molecular visualization tools to view the SwissDock results. Examples of popular visualization software include PyMOL, VMD, and UCSF Chimera.