To predict the effect of mutation on Protein Ligand Binding:

• Read in your PDB structure. The ligand and receptor have to be in the same object.
• Select the residue you wish to mutate
• Go to MolMechanics/Try Mutation/Protein Ligand Binding
• Select the ligand in the drop down menu.
• Select the amino acids you would like to try.
• Scan Pocket Surface This option will try a single residue side-chain mutation at each position in the protein that is in contact with the receptor.
• Keep All Chains will maintain the full PDB file in the results table.

Results

• A table will be displayed with the calculated ddG(kcal/mol) for each mutation selected.