SwissDock

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
[フレーム] Hide the sketcher
You submitted a ligand file. The latter will be treated as is, and atom naming will be kept when possible. However, if you modify the molecule in the sketcher, the atom naming and the molecular conformation provided in the Mol2 file will not be use during the parameterization.
. . . 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)
Choose chain(s) to keep*:

Choose heteroatom(s) to keep*:
Please do not select chemical solvent.
. . . 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
Controls:
  1. Mouse left-button + drag: rotate the system
  2. Mouse right-button + drag: translate the system
  3. Mouse wheel up and down: zoom and unzoom
  4. Mouse wheel click + drag: move near clipping plane and far fog
  5. Hitting "i" key: roll the system. Hitting "i" again stop the rolling.
  6. Hitting "k" key: rock the system. Hitting "k" again stop the rocking.

A double-click on a residue will center the view on this residue, while displaying it in ball and stick and the close neighbours in licoRICe.

A single-click on a residue will add a box on it.

Hovering the mouse pointer on an atom will display the atom name, as well as the residue name and number above the 3D viewer.

It is possible to display several types of molecular interactions between the selected residue and its environment using the different options available below the 3D viewer. It is also possible to display the protein surface using the option below the 3D viewer.

Full screen viewing can be obtained by clicking on the icon.
You can reset the viewer by clicking on the "reset" button below it.
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
Hide extra parameters
Sampling exhaustivity
The sampling exhaustivity determines the initial ligand rotation angle. The lower the angle, the higher the number of ligand poses.

Values are:
  • low: 180°
  • medium: 90°
  • high: 60°

low

medium

high

Cavity prioritization
The threshold value for cavity detection determines which cavities are considered for docking. A value of 70 detects mainly deep binding clefts, while a value of 50 also places attractive points in shallower protein cavities.

Threshold value for cavity detection:
  • buried: 70
  • medium: 60
  • shallow: 50

buried

medium

shallow

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)

Advanced ligand search

Not found!

  1. Search a small molecule by name, PDB id, or by InChI
  2. Enter or press the search button
  3. Click on the molecule of your choice in the table
  4. Press the apply button

SMILES are given at pH 7.4


Advanced target search Select your search database:
Protein name*:

Not found!

Source organism:
Experimental method:
UniProtKB accession number (AC) or entry name (ID)*:

Not found!

PDB template:
UniProtKB accession number (AC)*:

Not found!

* required
  1. Search a target by name (mandatory). Optionally, add an source organism and/or an experimental method
  2. Enter or press the search button
  3. Click on the target of your choice in the table
  4. Press the apply button

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