9. References

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Czodrowski, Paul; Sotriffer, Christoph A.; Klebe, Gerhard (2007a): Atypical protonation states in the active site of HIV-1 protease: a computational study. In Journal of chemical information and modeling 47 (4), pp. 1590–1598. DOI: 10.1021/ci600522c.

[Czodrowski2007b]

Czodrowski, Paul; Sotriffer, Christoph A.; Klebe, Gerhard (2007b): Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments. In Journal of molecular biology 367 (5), pp. 1347–1356. DOI: 10.1016/j.jmb.2007.01.022.

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Neeb, Manuel; Czodrowski, Paul; Heine, Andreas; Barandun, Luzi Jakob; Hohn, Christoph; Diederich, Francois; Klebe, Gerhard (2014): Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme. In Journal of medicinal chemistry 57 (13), pp. 5554–5565. DOI: 10.1021/jm500401x.

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Steuber, Holger; Czodrowski, Paul; Sotriffer, Christoph A.; Klebe, Gerhard (2007): Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase. In Journal of molecular biology 373 (5), pp. 1305–1320. DOI: 10.1016/j.jmb.2007.08.063.

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Shelley, J.C.; Cholleti, A.; Frye, L; Greenwood, J.R.; Timlin, M.R.; Uchimaya, M., “Epik: a software program for pKa prediction and protonation state generation for drug-like molecules,” J. Comp.-Aided Mol. Design, 2007, 21, 681-691

[Epik2016]

Schrödinger Release 2016-3: Epik, Schrödinger, LLC, New York, NY, 2016.

[Amber2016]

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Chen, Yunjie, and Benoît Roux. “Constant-pH hybrid nonequilibrium molecular dynamics–monte carlo simulation method.” Journal of chemical theory and computation 11.8 (2015): 3919-3931.