PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1) based on the 3D structure.
For proteins without ligands both version should produce the same result.
The method is described in the following papers, which you should cite in publications:
-
Sondergaard, Chresten R., Mats HM Olsson, Michal 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 7, no. 7 (2011): 2284-2295. doi:10.1021/ct200133y
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Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537. doi:10.1021/ct100578z
See propka.ki.ku.dk for the PROPKA web server, using the tutorial.
Clone repository or unpack the tar ball and install with setuptools (note: if you don't have setuptools installed you will need an internet connection so that the installation procedure can download the required files):
cd propka-3.1
python setup.py install --user
This will install the propka31 script in your executable directory,
as configured for setuptools, for instance ~/.local/bin. You can
change the bin directory with the --install-scripts option. For
example, in order to install in my bin directory in my home
directory:
python setup.py install --user --install-scripts ~/bin
For the purposes of testing or development, you may prefer to install PROPKA as an editable module via PIP by running
pip install -e .
from within a virtual environment (e.g., via virtualenv).
- Python 3.5 or higher
- Clone the code from GitHub
python setup.py install --user- Run
propka31with a .pdb file (see Examples)
Calculate using pdb file
propka31 1hpx.pdb
Please see tests/README.md for testing instructions.
Please run these tests after making changes to the code and before pushing commits.
Please cite these references in publications:
-
Sondergaard, Chresten R., Mats HM Olsson, Michal 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 7, no. 7 (2011): 2284-2295.
-
Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.