PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions.

By M. Olsson, Chresten R. Søndergaard, M. Rostkowski, Jan H. Jensen. Journal of Chemical Theory and Computation, 2011

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Evidence for an Elevated Aspartate pKa in the Active Site of Human Aromatase* (2014, methodology): “The PROPKA3 method was used to estimate the pKa value of Asp309 in the available crystal structures of aromatase.”
Using PyMOL as a platform for computational drug design (2017, methodology): “The residue protonation states can be prepared with PropKa 37 plugin in PyMOL.”
A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2 (2022, methodology): “5.2, with the default PARSE force ﬁ eld, and the implemented PROPKA (Dolinsky et al., 2007; Olsson et al., 2011).”
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design (2021, positive): “51 Finally, addition of polar hydrogen atoms and conversion to PDBQT were performed with AutoDock Tools.”