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PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
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README.md

PROPKA 3.1

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.

  • 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.

See propka.ki.ku.dk for the PROPKA web server, using the tutorial.

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 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

Requirements

  • Python 2.7 or higher or Python 3.1 or higher

Getting started

  1. Clone the code from GitHub
  2. python setup.py install --user
  3. Run propka31 with a .pdb file (see Examples)

Examples

Calculate using pdb file

propka31 1hpx.pdb

Testing (for developers)

Please run Tests/runtest.py/ after changes 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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