PROPKA 3.2

PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.2 and later) 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
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

Installation

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 <source directory>
python setup.py install --user

This will install the propka32 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 the bin directory in the 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).

Requirements

Python 3.5 or higher

Getting started

Clone the code from GitHub
python setup.py install --user
Run propka32 with a .pdb file (see Examples)

Examples

Calculate using pdb file

propka32 1hpx.pdb

Testing (for developers)

Please see tests/README.md for testing instructions. Please run these tests after making changes to the code and before pushing commits.

References / Citations

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.

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