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)
  
• propka: Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pK_a Values
  
• ProteinPrepare:
  
• PypKa: a flexible Python module for Poisson-Boltzmann based pKa calculations (for proteins) (standalone)
  
• 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
  
• Reduce: tool for adding and correcting hydrogens in PDB files