Ligand docking using the Dock Ligands tool

To run the "Dock Ligands" tool:

        Toolbox | Drug Design (Image DrugDesign_closed_16_n_p) | Dock Ligands (Image dock_ligands_16_n_p)

The Dock Ligands tool takes a Molecule Table containing small molecules (ligands), and a Molecule Project containing a Binding Site Setup (see Setup Binding Site) as input. For each of the small molecules in the Molecule Table, the docking simulation searches for optimal binding modes to the binding site. The optimal binding mode together with a score of the binding mode are returned in a Docking Results Table (see Docking Results Tables). The docking algorithms are described in The docking algorithms.

In the Dock Ligands wizard step 1 (figure 10.55), select the Molecule Table that holds the small molecules to dock. More than one table can be selected at the same time.

Image dock_ligands_step1
Figure 10.55: The "Dock Ligands" dialog. Select the "Molecule Table" that hold the small molecules to dock.

Click on the button labeled Next to select the Molecule Project and specify the docking parameters (figure 10.56).

Image dock_ligands_step2
Figure 10.56: Select the "Molecule Project" with the binding site setup and specify the docking parameters.

This wizard has the following options:

Note! The wizard will remember the user defined settings from run to run. If you wish to bring the settings back to the default settings, this can be done by clicking on the small arrow button in the lower left corner of the dialog.

Click on the button labeled Next and consider whether the Docking Results Table should open when the docking is done, or if it should be saved in the Navigation Area. A log file of the simulation process can also be made.

If you choose to save the results, the next step will allow you to specify where to save it, otherwise click on the button labeled Finish, and the docking simulation will start. You can see how it proceeds in the Processes tab in the Toolbox area.