Excluded Volumes from Reference Structures Dialog Box

Create excluded volumes in a full or partial shell around one or more reference structures.

To open this dialog box, click Reference Structures in the Manage Excluded Volumes panel.

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  • Features
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Using the Excluded Volumes from Reference Structures Dialog Box

Placing excluded volumes around a reference ligand or set of ligands is one way of simulating the presence of a receptor. (If you have a receptor, you can use the Excluded Volumes from Receptor dialog box to place excluded volumes).

Using just the reference ligand, the excluded volume shell is a complement to the molecular volume, so a search with this kind of shell should produce similar results to a shape search. Likewise, placing a shell around several active ligands should produce results similar to a shape search with multiple query structures.

If you have a set of active ligands in which parts of the structures overlap very well, but other parts vary in the region of space they occupy, you might conclude that the variable region is solvent-exposed, and then place a shell around only the highly aligned region. You can do this by picking the parts of the ligands that you want to use to create the shell.

To set up the excluded volumes, you must first align the ligands you want to use to the hypothesis. You can use the Phase Ligand Screening Panel with your ligands, and use the hit file for the aligned ligands, or use the phase_find_matches utility.

Excluded Volumes from Reference Structures Dialog Box Features

Shell source options

Select an option for the atoms around which to create the shell of excluded volumes.

Hypothesis reference ligand

Create a full shell of excluded volumes around the reference ligand for the hypothesis. When running from the Develop Common Pharmacophore Hypotheses panel, the hypothesis is the one that is included in the Workspace.

Selected atoms

Create a partial shell of excluded volumes, around the atoms that are selected in the Workspace. These atoms should be part of one or more ligands that are aligned to the hypothesis. The atoms can be selected with the Pick shell atoms picking tools.

Minimum distance between ligand surface and shell text box

Specify the minimum distance between the van der Waals surface of any of the ligands used and the surface of an excluded volume sphere, in angstroms. This buffer distance can be considered to simulate receptor flexibility.

Excluded volume sphere radii text box

Specify the radius that is to be used for the excluded volume spheres. Using a larger radius produces less spheres, but results in a less well-defined shape for the excluded region.

Create Excluded Volumes button

Click this button to run the application that creates the excluded volumes and close the dialog box. When the application finishes, the excluded volumes are added to the table in the Manage Excluded Volumes Panel.

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