PURPOSE: It is often useful to determine the surface area of a protein cavity that may be a known or potential binding site. A common way to accomplish this is to determine the amino acid residues that are within a specified radius of a docked ligand inside the cavity or DS binding site object and then calculate the Solvent Accessible Surface Area (SASA) of those residues. However, some of those residues may have exposed regions that are not part of the cavity and that area will be included in such a calculation. This script ensures that only the area inside the cavity is calculated.

This script is intended to work on a receptor molecule in which binding site objects have been defined. It assumes that you have either selected one binding site object or have only one binding site object visible. It then converts the binding site points into (potassium) atoms. It calculates the Solvent Accessible Surface Area for all the amino acid residues in the receptor both in the presence of the binding site atoms and in their absense. The difference is the surface area of atoms lining the cavity. This area is reported in the standard output of the script as well as in the BindingSite tab of the data table as the 'Cavity SASA' of the selected/visible binding site object.

INSTALLATION: Save BindingPocketSASA.pl to a local directory or location accessible from the Files Explorer

USAGE:

From the DS Client: From the Files Explorer, double-click on the BindingPocketSASA.pl to launch the script or right-click on the file and select Open With | Script Window then launch the script using the Run command from the Scripting toolbar.

DISCLAIMER: This custom script is compatible with Discovery Studio 2.5.5 and 3.0. It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.

REQUIREMENTS: This script will run on the most recently view Molecule Window. It assumes that you have a binding site object visible and/or selected.

EXPECTED RESULTS: The calculated cavity SASA is reported in the Output View of the Script Window and is added to the BindingSite tab of the data table as a new property called 'Cavity SASA'.

The attached .zip contains:
1. The BindingPocketSASA.pl DiscoveryScript