58 lines
2.0 KiB
Markdown
58 lines
2.0 KiB
Markdown
# PROPKA 3.1
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PROPKA predicts the pKa values of ionizable groups in
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proteins (version 3.0) and
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protein-ligand complexes (version 3.1)
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based in the 3D structure.
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For proteins without ligands both version should produce the same result.
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The method is described in the following papers, which you should cite
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in publications:
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* Søndergaard, 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.
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* Olsson, Mats HM, Chresten R. Søndergaard, 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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See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
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using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial).
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## Installation
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No installation needed. Just clone and run.
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## Requirements
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* Python 3.1 or higher
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## Getting started
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1. Clone the code from GitHub
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2. Run 'propka.py' with a .pdb file (see Examples)
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## Examples
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Calculate using pdb file
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./propka.py 1hpx.pdb
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If for some reason your setup with python3.1+ is
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not located in '/usr/bin/python3', run the script
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python3.2 propka.py 1hpx.pdb
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## Testing (for developers)
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Please run `Tests/runtest.py/` after changes before pushing commits.
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## References / Citations
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Please cite these references in publications:
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* Søndergaard, 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.
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* Olsson, Mats HM, Chresten R. Søndergaard, 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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