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Article ID: 119 - Last Modified: May 4, 2011

I want to calculate the interaction energy between a residue and another chain in a protein/antibody. What program or script can I use?

Please download and install the script component_interactions.py from our Script Center. Open the script from Scripts → Molecular Mechanics → Component Interactions. In the Atom Sets tab, click on the Chain-Residue tab. Click on the chain to mark it as Set1, and then click 'Create Sets'. This Set1 definition will be used to identify the residues from the other chain that are in proximity. Currently, this can only create 40 sets (1 set is Set1, followed by 39 residues that are in proximity to Set1). In the Properties tab, select 'All interaction energy terms' and check the box in front of 'Write Set1 SASA contribution csv file'. This will write out the individual energy contribution terms and also the SASA terms. Lastly, we have also observed good results using a distance-dependent dielectric model instead of a constant dielectric. You can change this option from the Potential tab under 'Electrostatic Treatment'. Lastly, click the Start button. This will run a Macromodel single point energy calculation, and report the results in CSV format with the following terms: Contact area, exposed area, Percent (contact/exposed), Total interaction energy, Vdw interaction energy, Electrostatic Interaction Energy. It will also color the Workspace with the Total interaction energies and update the Project Table.

Keywords: protein protein interaction, antibody modeling, protein modeling, biologics

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