Welcome to the new SwissDock, based on the Attracting cavities and Autodock Vina docking engines.
Please, note that the old version, based on EADock DSS, is still available at the address http://old.swissdock.ch and will be maintained for several months. Consider transitioning your projects from the old to the new server. Thank you!
Don't know where to start? Try with an example: binding of SNJ-1715 (PDB ID 0m6) to calpain-1 catalytic subunit (PDB ID 2g8e), of WRR-99 (r99) to cruzipain (1ewl), or of dabrafenib (p06) to B-Raf (5hie).
1 - Submit a ligand
Provide a SMILES 
. . . or upload a Mol2 file or a PDBQT file
Please provide a file containing only 1 molecule, with all hydrogens and 3D coordinates
. . . or input, or modify, or check the molecule using the sketcher
. . . or use the advanced search
   Reset ligand
2 - Submit a target
Provide a PDB id (e.g. 5hie)  
. . . or upload a PDB file or a PDBQT file  
. . . or use the advanced search
   Reset target
3 - Define search space
Search box center Å
Search box size Å
Hydrogen bonds
Ionic interactions
Cation-π interactions
Hydrophobic contacts
π-stacking interactions
Show protein surface
∅
4 - Select parameters
Number of RIC
The number of Random Initial Conditions (RIC) to be generated.

1

2

3

4

5

6

7

8
Show extra parameters
Sampling exhaustivity
Increase the sampling exhaustivity to increase the amount of computational effort.
  
Before a docking, we need to check your parameters. We check if the grid contains attractive points and if your job will not take too much time.
The computational time depends on:
  • the box size
  • the sampling exhaustivity
  • the cavity prioritization (Attracting Cavities only)
  • the number of random initial conditions (RIC) (Attracting Cavities only)
If you want to reduce the estimated time, reduce the number of RIC or the box size, decrease the sampling exhaustivity and/or the cavity prioritization.
(Prepare ligand and target)
5 - Start docking
Enter an email (optional)
Enter a docking name (optional)
   Reset form

(Check your parameters before)