Skip to main content
. Author manuscript; available in PMC: 2015 Jun 25.
Published in final edited form as: J Comput Chem. 2014 Apr 22;35(16):1255–1260. doi: 10.1002/jcc.23616

Figure 3.

Figure 3

Snapshot of example for estimating the protein's desolvation free energy associated with replacing the water molecules in the protein binding site on ligand binding. a) Dialog for importing ligand library and define hydration site selection radius. b) Results for desolvation free energy estimation. c) Snapshot of PyMOL viewer window associated with the desolvation free energy estimation. One ligand (cmp1) is shown in stick representation. The hydration sites that are within 1 Å to any of cmp1's heavy atoms were selected as “cmp1_replacedHS” and shown as spheres.