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.
Create figures for your articles
Propose a binding mode for a ligand
Generate a complex to perform subsequent calculations
Design inhibitors for the target of your choice
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.
SwissDock and S3DB are developed by the Molecular Modeling Group of the Swiss Institute of Bioinformatics in Lausanne, Switzerland.