The PROPKA Web Interface
Download the PROPKA source code and scripts: PROPKA Download.
PROPKA plug-in for VMD can be downloaded here
(Please report errors here.)
The PROPKA method is developed by the
Jensen Research Group
Department of Chemistry
University of Copenhagen
Please cite these references in publications:
If you use the PROPKA GUI please cite this reference:
Reprints can be obtained by contacting Jan
- 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
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
Last Updated November 23th, 2012