PURPOSE: Creates a binding site object at each cavity of a protein. Sums the hydrophobicity of the residues within 3 angstrom of each binding site and if the sum is > 1.0 the cavity is considered hydrophobic and all waters within 3 angstrom of the binding site object are deleted. Each Cavities' total hydrophobicity is reported to the standard output (i.e. the Output view of the Script Window). All deleted water residue names are also reported to the standard output.
When a cavity is defined as hydrophobic all residues which line the cavity are added to a new group with the name Hydrophobic_Cavity_ followed by an incremented number. Finally, the script modifies atom colors so that most protein atoms are colored green and only those atoms in the hydrophobic cavities are colored by their residue's hydrophobicity value.

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

USAGE: From DS Client: Open a file containing a protein molecule. From the Files Explorer, double-click on the remove_waters_hydrophob_cav.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 2.0. 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.

EXPECTED RESULTS: When this script is executed on 1kim.pdb the output will be the attached 1kim_hydrophobic_cav.msv

The attached .zip contains:
1. A README.txt
2. The remove_waters_hydrophob_cav.pl DiscoveryScript
3. A sample output file called 1kim_hydrophobic_cav.msv