A python module for flexible Poisson-Boltzmann based pKa calculations.

We have implemented a flexible tool to predict Poisson-Boltzmann-based pKa values of biomolecules. This is a free and open source project that provides a simple, reusable and extensible python API and CLI for pKa calculations with a valuable trade-off between fast and accurate predictions. With PypKa one can enable pKa calculations, including optional proton tautomerism, within existing protocols by adding a few extra lines of code. PypKa supports CPU parallel computing on anisotropic (membrane) and isotropic (protein) systems and allows the user to find a balance between accuracy and speed.

PypKa is written in Python and Cython and it is integrated with the Poisson-Boltzmann solver DelPhi Fortran77 via DelPhi4Py.

If you use PypKa in your research please cite the following paper:

Reis, P. B. P. S., Vila-Viçosa, D., Rocchia, W., & Machuqueiro, M. (2020). PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations. Journal of Chemical Information and Modeling, 60(10), 4442–4448.

author = {Reis, Pedro B. P. S. and Vila-Viçosa, Diogo and Rocchia, Walter and Machuqueiro, Miguel},
title = {PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations},
journal = {Journal of Chemical Information and Modeling},
volume = {60},
number = {10},
pages = {4442-4448},
year = {2020},
doi = {10.1021/acs.jcim.0c00718}


PypKa can be easily installed using the pip package manager.

Source code is freely available at GitHub under the LGPL-3.0 license. The package can be installed from PyPi.


Please submit a github issue to report bugs and to request new features.

Alternatively you may find the developer here . Please visit our website for more information.