Continuum electrostatics pKa calculations

David Sept

Washington University in St. Louis
Department of Biomedical Engineering
Center for Computational Biology

Nathan Baker

Washington University in St. Louis
Department of Biochemistry and Molecular Biophysics
Center for Computational Biology

Copyright © 2004, 2005 by Washington University in St. Louis

Table of Contents
Introduction
pKa review
Amino acid model pKa values
pKa values in proteins
Continuum electrostatics methods for pKa calculations in proteins
Application to lysozyme
Background
Preparing the PDB file
Setting up the total electrostatic energy calculations
Setting up the transfer free energy calculations
Putting it all together
Additional pKas and questions
List of Equations
1. Acid dissociation free energy
2. Transfer free energy
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