Article ID: 361 - Last Modified: May 3, 2012
Is it possible to prepare a protein at a user-defined pH?
As of Suite 2012, you can set the protein pH in the Refine tab of the Protein Preparation Wizard. The PROPKA package is used to determine the protonation state of the protein. You can also use simplified rules for four different pH ranges instead of a pH value. These simplified rules are also available in Suite 2011. The ligand pH can be set in the Review and Modify tab, and you can choose the state that you prefer.
For earlier releases, the Protein Preparation Wizard does not support setting receptor protonation states appropriate for user-defined pH values. You will have to adjust these residues yourself. The Interactive Minimizer lets you choose the protonation states of ASP, GLU, and HIS, so you could adjust these residues as needed.
Keywords: protein preparation, user-defined pH, Maestro
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