A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules.

@article{Myers2006ASC,
  title={A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules.},
  author={Jonathan B. Myers and Greg Grothaus and Shivaram Narayanan and Alexey Onufriev},
  journal={Proteins},
  year={2006},
  volume={63 4},
  pages={
          928-38
        }
}
Structure and function of macromolecules depend critically on the ionization states of their acidic and basic groups. Most current structure-based theoretical methods that predict pK of ionizable groups in macromolecules include, as one of the key steps, a computation of the partition sum (Boltzmann average) over all possible protonation microstates. As the number of these microstates depends exponentially on the number of ionizable groups present in the molecule, direct computation of the sum… CONTINUE READING

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