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. Author manuscript; available in PMC: 2012 Jan 24.
Published in final edited form as: J Chem Inf Model. 2010 Nov 30;51(1):69–82. doi: 10.1021/ci100275a

Figure 3.

Figure 3

The correlation between the best performed solute dielectric constants and the PSASAD values for six complexes, α-thrombin/a1, avidin/b1, cytochrome C peroxidase/c1, neuraminidase/d1, P450cam/e1 and penicillopepsin/f1. PSASAD was calculated based on a cutoff of (a) 5 Å or (b) 6 Å to define polar/polar interactions between the protein and the ligand. In this figure, the solute dielectric constant εin is 1 for avidin, cytochrome C peroxidase and P450cam, 2 for penicillopepsin and α-thrombin, and 4 for neuraminidase. For α-thrombin, εin= 4 is chosen based on the correlation coefficient; but as noted in the text, εin= 1 or 2 may be a better choice for ligands a1 to a4.