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This website is beta. User experience may be inconsistent and docking submission may be broken from time to time.


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.

How?

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

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

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

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

  • the most favorable clusters are dumped in a file.

Who?

SwissDock and S3DB are developed by the Molecular Modeling Group of the Swiss Institute of Bioinformatics in Lausanne, Switzerland.

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

Citing?

A manuscript for you to cite is being written for EADock DSS and this website.
In the meantime, if you use this webservice, please contact us and mention its URL in your work.

For more details about EADock, please see the articles presenting its algorithm [1, 2, 3, 4] and some of its applications [1, 2, 3, 4, 5, 6].

A manuscript for you to cite is being written. In the meantime, if you use this webservice, please, mention its URL in your work.

This server is free for academic use. A CHARMm license is required for users from private companies.