Protonation

• DeepKa: deep-learning-based protein pKa predictor (online)

  

  

• H++: automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment (online)

  

  

• PDBFixer: application for fixing problems in PDB - Protein Data Bank files, missing residues, loop... (standalone)
  

• ProToss: predict tautomers and protonation states in protein-ligand complexes

  

  

• ProteinPrepare:

  

• PypKa: a flexible Python module for Poisson-Boltzmann based pKa calculations (for proteins) (standalone)
  

  

• Reduce: tool for adding and correcting hydrogens in PDB files
  

• propka: Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values
  

  

• pypka: allows users to run physics-based, as well as ML-accelerated methods suitable for larger systems, to obtain pKa values, isoelectric points, titration curves, and structures with representative pH-dependent protonation states compatible with commonly used force fields