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Article ID: 1428 - Last Modified: July 24, 2013

How can I assign proper protonation states to residues in a protein (e.g., during the preparation process)? Is there a Schrödinger program to predict protein residue pKa?

Starting with Suite 2012, Schrödinger offers access to the PROPKA program for prediction of the pKa of protein residues, via the Protein Preparation Wizard. You can run this program in the Refine tab and label residues by their pKa values by selecting "Use PROPKA" and "Label pKas".

The Protein Preparation Wizard also alters residue ionization/tautomer states, as part of optimizing H-bond networks, and relative penalties for different protonation states obtained from pKa estimates are part of the optimization process. With the Interactive Optimizer, you can adjust the state of individual residues, if desired.

For more information on PROPKA, visit the PROPKA web site:

http://propka.ki.ku.dk/

You can also download the software from this site if you are still using a release earlier than 2012.

Keywords: protonation state assignment

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