PURPOSE: This script can be used to analyze the various properties of amino acid residues at the interface between 2 or more chains and to elucidate the interactions occurring at that interface. The script acts upon an active Molecule Window with a molecule containing 2 or more chains and a group which defines one set of chains.
It then :
* Defines a second group which consists of all residues NOT in the first (specified) group
* Defines the bindingsite residues that are sitting in the interface within 6 A of the 2 groups
* Calculates the surface area (SA) for each bindingsite residue both in complex and unbound
* Calculates the percentage of the buried SA
* The contact surface area is the difference between the unbound and complexed SA (note, a probe radius of 0.6 angstrom is the default)
* Calculates interaction energy contributed by each bindingsite residues (Calling the Calculate Interaction Energy protocol)
* Determines the number of side chain rotatable bonds for each bindingsite residue
* Writes out the per residue values of the 'Contact SA', 'Percent Buried SA', 'InComplex SA', 'Num SC Rot Bonds', 'Total Interaction Energy', 'Vdw Interaction Energy' and 'Electrostatic Interaction Energy' to the Amino Acid and/or Residue Tab of the Data Table (for each bindingsite residue).
* Writes out the above values for the Amino Acids to a separate csv file.
The script will work if the molecule consists of a protein-protein complex or protein-ligand complex. The user can specify whether to use a Distance-Dependent Dielectric during the Interaction Energy calculation (see lines #81-82).

INSTALLATION: Save ResContactSASInterE.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 ResContactSASInterE.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. 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 viewed Molecule Window. The window should contain a 'molecule' with 2 or more chains and a group which defines one set of chains(s). The default name of this group is 'ligand' but can be modified at line #67
*** Adjustable parameter are found at lines 64 through 85. Refer to comments in that section for parameter description.

EXPECTED RESULTS: Various Residue/AminoAcid attributes added to the Data Table as well as an output .csv file.

The attached .zip contains:
1. A README.txt
2. The ResContactSASInterE.pl DiscoveryScript