Glide WS - Docking Panel

Dock ligands to a Glide WS model, which includes an ensemble of protein structures for assessment of small induced fit effects and protein reorganization. The scoring includes terms for water displacement and desolvation effects, molecular recognition (H-bonds, hydrophobic enclosure, etc), ligand strain, salt bridges.

To open this panel, click the Tasks button and browse to Receptor-Based Virtual Screening → Glide WS Docking.

  • Using
  • Features
  • Additional Resources

Using the WS - Docking Panel

As for any docking experiment, the ligands must be properly prepared beforehand. We recommend using LigPrep, and including the Epik state penalties.

The following reference describes Glide WS, and should be cited when Glide WS is used.

Robert B. Murphy, Matthew P. Repasky, Jeremy R. Greenwood, Ivan Tubert-Brohman, Steven Jerome, Ramakrishna Annabhimoju, Nicholas A. Boyles, Christopher D. Schmitz, Robert Abel, Ramy Farid, and Richard A. Friesner J. Med. Chem. 2016, DOI: 10.1021/acs.jmedchem.6b00131.

Glide WS - Docking Panel Features

Model section

Specify the Glide WS model to be used for docking. Click Browse to navigate to the model, which is stored in a zip archive (.zip), or enter the path in the File text box. The default name given to the model zip archive is jobname_models.zip.

Ligands to be docked section

Specify the ligands to be docked.

NOTE: It is recommended that you prepare the ligands before docking (for example, with LigPrep or MacroModel).
Use ligands from options

Select the source of the ligands, from the following options:

  • File—Dock ligands from a file. Enter the file name in the File text box, or click the Browse button to navigate to the ligand file.

    By default, all structures in the file are docked. To specify a particular range of ligands, use the Range controls:
    To start at a ligand other than the first, edit the value in the first text box.
    To end at a value other than the last, deselect End and edit the value in the second text box.

    If a docking job terminates abnormally, you can set the initial ligand number to pick up after the point in the input ligand file at which the problem occurred.

  • Selected entries—Dock ligands that are selected entries in the Project Table. For more information about the Project Table and entry selection, see the Project Table Panel topic.

  • Workspace—Dock the structures in the Workspace. If you select this option, the entries in the Workspace must all be valid ligands, as described above.

Use input partial charges option

Select this option to use partial charges from the input structures instead of those from the force field. This option enables you to use improved partial charges, for example from a Jaguar or a QM-Polarized Ligand Docking calculation.

Do not dock or score ligands with more than a atoms text box

Set the maximum number of atoms a ligand structure may have if it is to be docked. Ligand structures in the input file that have more than the specified number of atoms are skipped. The default (and maximum) is 500 atoms. You can reduce the maximum number of atoms a, if the active-site region is small and enclosed, to speed up a docking calculation on a large ligand database.

Do not dock or score ligands with more than r rotatable bonds text box

Set the maximum number of rotatable bonds a ligand structure may have if it is to be docked. Ligand structures in the input file that have more than this number of rotatable bonds are skipped. The default number is 50 rotatable bonds. If only relatively small or rigid ligand "hits" are wanted, you can decrease the value of r.

Docking section

This section allows you to make settings for the docking stage of model generation.

Add Epik state penalties to docking score option

Add penalties for ionization and tautomeric states to the docking score. To use this option, the ligand preparation process must have included state generation by Epik. This means that if you use the LigPrep panel to prepare ligands, you must select Epik under Ionization and Generate tautomers for tautomerization.

Sample macrocycles using Prime option

Generate macrocycle ring templates on the fly and increase the number of conformers and poses sampled by Glide. Non-macrocycle ligands will be skipped.

Advanced Options button

Adjust Glide WS parameters for the chosen ensemble. Opens the Advanced Options dialog box.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

Settings for distribution of the job over subjobs are available in the Job Settings Dialog Box.

The Job Settings button opens the Glide WS - Docking - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Tutorials

Related Topics