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Article ID: 119 - Last Modified:

I want to calculate the interaction energy between a residue and another chain in a protein/antibody. How can I do this?

You can calculate interaction energies between residues with the Prime Energy Visualization tool (Tasks → Protein Analysis → Energy Visualization in the Maestro interface, Tasks → Implicit Solvent Refinement + Analysis → Visualize Energy in the BioLuminate interface). The results can be displayed graphically in the Workspace, colored by the strength of the interaction between a selected residue and other residues. If you want the actual values of the interaction, they are available in the log file for the Prime job.

If you want to determine the effect of mutating a residue on the binding free energy of two proteins (an antibody and an antigen, for example), you can use the BioLuminate Residue Scanning tool (Tasks → Residue Scanning in the BioLuminate interface). This tool allows you to select residues to mutate and define the mutations and the binding partners. You can also optimize the binding affinity. The results for the mutated structures are presented in a panel which allows you to examine the values and also visualize the results.

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