Article ID: 733 - Last Modified: April 18, 2012
What procedure do I follow if I want to mutate amino acid residues?
You can mutate an amino acid residue by right-clicking on the residue in the Workspace and choosing Mutate → new-residue. If you want to keep the original structure, you can duplicate it in the Project Table, then mutate the duplicate structure. To find the residue in the Workspace, type CTRL+F to display the Find toolbar, choose Residue number from the option menu, and type the residue number in the text box (e.g. A:167), then click the N (next) button.
After you have performed the mutation, you should check that the side chain is in a suitable conformation. If it is not, you can right-click on the residue and choose Rotamers, to choose from the common side-chain rotamers. Alternatively, you can manually adjust the side chain. To relax the structure around the mutation, choose the mutated residue and its neighbors, and press CTRL+M for a short minimization.
If you have prepared the original structure with the Protein Preparation Wizard, it is probably not necessary to do so again; however it could be important to optimize the H-bond network, and to run the restrained minimization.
If there is a substantial size difference between the original and the new residue, or the side chain is not oriented correctly, you might need to use a Prime side-chain prediction to find a good conformation for the new residue and its neighbors.
If you expect more substantial changes in the receptor or the ligand pose with the mutation, you might need to run IFD to generate some alternative receptor conformations and ligand binding modes.
Keywords: mutate, Maestro, Glide, amino acid
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