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Using SwissDock Stable.
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What?

This website provides an access to:

  • SwissDock, a web service to predict the molecular interactions that may occur between a target protein and a small molecule.

  • S3DB, a database of manually curated target and ligand structures, inspired by the Ligand-Protein Database.

Would you like to organize a workshop? Please let us know so that we can adjust the computing resources accordingly.

Why?
  • Propose a binding mode for a ligand

  • Create figures for your articles

  • Generate a complex to perform subsequent calculations

  • Design inhibitors for the target of your choice

How?

SwissDock is based on the docking software EADock DSS, whose algorithm consists of the following steps:

  1. many binding modes are generated either in a box (local docking) or in the vicinity of all target cavities (blind docking).

  2. simultaneously, their CHARMM energies are estimated on a grid.

  3. the binding modes with the most favorable energies are evaluated with FACTS, and clustered.

  4. the most favorable clusters can be visualized online and downloaded on your computer.

EADock DSS

Who?

SwissDock and S3DB are developed by Aurélien Grosdidier, Vincent Zoete and Olivier Michielin, from the Molecular Modeling Group of the Swiss Institute of Bioinformatics in Lausanne, Switzerland.

Calculations are performed on the Vital-IT cluster (status)

EADock and SwissDock have been funded by the FNS project grant #310030_130857 and the Swiss Institute of Bioinformatics

Links?

You can easily create direct links to the SwissDock submission form, preloaded with protein and ligand structures defined as URLs:

Sample link

Inspect the source code of this page to see how easy it is !

Cite?

This server is free for academic use. A CHARMm license is required for users from private companies.
Please contact us if you need your own private SwissDock service.