[ On-screen Demo Dock | Batch Docking | Run Docking Batch | Dock Chemical Table ]

Once the receptor and maps are ready, select a docking workflow. Some options require ICM-VLS.

• On-screen Demo Dock is ideal when you have a single ligand and simply want to re-dock it to the receptor. For anything more advanced, such as multiple ligands or larger workflows, use Batch Docking or Dock Chemical Table (see below). It can also be used to view the ligand docking to the pocket which is useful for teaching or demonstration purposes. In ICM versions 3.8-5 and older this option was called Interactive Docking.
• BATCH docking will run in the background and is an ideal choice for screening a database of compounds e.g. vls.
• Dock Chemical Table allows you to dock a chemical spreadsheet / sdf file that is loaded into ICM.

[ Mol Table Ligand | Loaded Ligand ]

Use Docking/On-screen Demo Dock to dock a single ligand and display its sampling in the binding pocket, for teaching or demonstrations. For routine research, use Dock Chemical Table or Batch Docking.

With the receptor and maps prepared, choose one of the ligand sources below and enter the Docking Project Name. Both sources share these settings:

• Effort/Thoroughness: Controls simulation length. A value of 1 is a reasonable starting point for buried hydrophobic pockets; consider increasing it for solvent-exposed pockets or sites containing metal ions.
• Display run: Shows ligand sampling in the pocket but slows the calculation.
• Docking score: Requires ICM-VLS.

Open a MOL, MOL2, or SDF file using File/Open to load a chemical table. Select the table and enter the ligand's row number (for example, 6 for the compound in row 6).

Select a ligand already loaded as an ICM object. By default, sampling starts at the pocket center; optionally use the ligand's existing position if it is already in the pocket.

The simulation can also be saved to a trajectory file; see the command language manual for details.

[ From Loaded ICM Object | From File | From Mol/Mol2 | From Indexed Database | From MolCart Database ]

Batch docking runs in the background and is suitable for large-scale docking and virtual screening. Choose Docking/Setup Batch Ligand, select an input source below, and enter the docking project name where requested. Click OK to save the setup, then proceed to Run Docking Batch.

For a ligand already loaded as an ICM object, select Ligand Molecule from the drop-down list or enter an ICM selection. Keep the default Ligand Name or enter a new name for the docked ligand.

Browse to a saved ICM object file. The object does not need to be loaded beforehand.

Browse to the ligand file and select MOL or MOL2 format. Enable hydrogen addition and charge assignment as needed.

Requires ICM-VLS. First create an index for the SDF or MOL2 database as described in Database File Format. Select the index file and molecular file format, then enable hydrogen addition and charge assignment as needed.

Requires ICM-VLS and a separate MolCart license. Enter the server, username, password, database name, and table name. Enable hydrogen building and 2D-to-3D conversion as needed.

After setting up the ligand input, select Docking/Run Docking Batch to start docking or virtual ligand screening in the background. Choose Local VLS to run locally, or VLS via Queueing System to use a queuing system.

For Local VLS, review the following settings:

• Project name: Select the prepared docking project.
• Output file suffix: Enter a suffix for the output files, for example answers.
• Docking effort: Controls the length of the docking search. A value of 1 is a reasonable starting point for buried hydrophobic pockets; consider increasing it for solvent-exposed pockets or sites containing metal ions.
• Store Alternative Conf.: Save alternative ligand conformations in the energy stack for inspection.
• Score All Stack Conf.: Calculate an ICM docking score for all stored conformations. This increases calculation time.
• licenseType: Leave set to default unless your license requires a specific option. If unsure, contact support@molsoft.com.
• Use Score Filter: Enable filtering by docking score and enter the required Score Cutoff. More negative docking scores indicate more favorable scores.
• Number Of Parallel Jobs: Set the number of docking jobs to run concurrently. Choose a value appropriate for the available computing resources and license.
• Use Range: Process a specified range of input entries. Enter the first and last entry numbers in From entry and To entry; leave unchecked to process the full input.

Click OK to start. Use Windows/Background Jobs to monitor the calculation.

To dock directly from a chemical table:

Setup the receptor and read in the chemical table.

Select the chemicals in the table you wish to dock. If no selection is made ICM will dock the whole table. You can make selections by clicking on the row numbers whilst holding CTRL (non-contiguous selection) or TAB (contiguous selection).

Click on the Docking menu and select Dock Chemical Table. To change the default docking options, uncheck Dock Immediately. This will display a panel next to the chemical table where you can adjust settings, such as increasing the number of conformations to save. Then click Dock in the tools panel.

Once the docking has finished a hitlist will be displayed.