The PROPKA Web Interface

Download the PROPKA source code and scripts: PROPKA Download.
PROPKA plug-in for VMD can be downloaded here

The PROPKA method is developed by the
Jensen Research Group
Department of Chemistry
University of Copenhagen

Please cite these references in publications:

• Hui Li, Andrew D. Robertson, and Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of Protein pKa Values" Proteins, 2005, 61, 704-721.
• Delphine C. Bas, David M. Rogers, and Jan H. Jensen "Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes" Proteins, 2008, 73, 765-783.
• Mats H.M. Olsson, Chresten R. Søndergard, Michal Rostkowski, and Jan H. Jensen "PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions" Journal of Chemical Theory and Computation, 2011 7 (2), 525-537
• Chresten R. Søndergaard, Mats H.M. Olsson, Michaz Rostkowski, and Jan H. Jensen "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values" Journal of Chemical Theory and Computation, 2011 7 (7), 2284-2295

• Michal Rostkowski, Mats HM Olsson, Chresten R Søndergaard and Jan H Jensen "Graphical Analysis of pH-dependent Properties of Proteins predicted using PROPKA" BMC Structural Biology 2011 11:6.

Use PROPKA and PDB2PQR to add hydrogens to your x-ray structure: PDB2PQR

The PROPKA web interface was created by Donald Ephraim Curtis with help from Todd Dolinsky and Nathan Baker
PROPKA 2.0 added by David M. Rogers
PROPKA 3.0 and 3.1 added by Chresten R. Søndergaard