PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations
datasetposted on 16.09.2020 by Pedro B. P. S. Reis, Diogo Vila-Viçosa, Walter Rocchia, Miguel Machuqueiro
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
The protonation of titratable residues has a significant impact on the structure and function of biomolecules, influencing many physicochemical and ADME properties. Thus, the importance of the estimation of protonation free energies (pKa values) is paramount in different scientific communities, including bioinformatics, structural biology, or medicinal chemistry. Here, we introduce PypKa, a flexible tool to predict Poisson–Boltzmann/Monte Carlo-based pKa values of titratable sites in proteins. This application was benchmarked using a large data set of experimental values to show that our single structure-based method is fast and has a competitive performance. This is a free and open-source tool that provides a simple, reusable, and extensible Python API and CLI for pKa calculations with a valuable trade-off between fast and accurate predictions. PypKa allows pKa calculations in existing protocols with the addition of a few extra lines of code. PypKa supports CPU parallel computing on solvated proteins obtained from the PDB repository but also from MD simulations using three common naming schemes: GROMOS, AMBER, and CHARMM. The code and documentation to this open-source project is publicly available at https://github.com/mms-fcul/PypKa.