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. Author manuscript; available in PMC: 2013 Jul 25.
Published in final edited form as: J Chem Theory Comput. 2012 Jul 25;8(9):3022–3033. doi: 10.1021/ct3003817

Fig. 2.

Fig. 2

The thermodynamic cycle that we used in our calculations. The horizontal arrows represent free energy differences upon mutation of the solute (ILE side chain analog and GLN side chain analog). The vertical arrows represent the solvation process, i.e. the solute is brought from vacuum into solution. For each free energy calculation the colored circles highlight which atoms are considered “P” (black), “N” (blue) or “M” (red).