Very fast prediction and rationalization of pKa values for protein–ligand complexes

By Delphine Bas, D. Rogers, Jan H. Jensen. Proteins: Structure, Function, and Bioinformatics, 2008

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CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction (2018, neutral): “pKa: the pKa value predicted by the PROPKA program (30); QSASA: the exposure degree of the cysteine, which is calculated by dividing the solvent accessible surface area (SASA) of this cysteine with the theoretical SASA, which is calculated by the Pops program (31).”
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA (2011, background): “PROPKA [7-9] is one of the popular protein pKa prediction software packages mainly because of its speed and accuracy compared to other methods [4,6], but also because it offers a structural rationalization of the predicted pKa values.”
A practical guide to large-scale docking (2021, methodology): “7), Maestro (Schrödinger) 48 , PropKa 49 or Chimera 50 can be used to protonate the target of interest.”
AlphaFold2 models indicate that protein sequence determines both structure and dynamics (2022, background): “The protonation states of all titratable residues of the protein were determined by ProPka 43 at neutral pH of 7.”