the entropic loss for immobilizing the water involved [10]. Thus,
the thermodynamics of water molecules in protein active sites is
important for understanding protein–ligand interactions for drug
design. A well-known example of water mediated protein–ligand
interaction is found among HIV-1 protease inhibitors (Fig.1)
[9, 14]. A conserved water molecule (water 301) is located on the
HIV-1 protease symmetry axis. This water molecule forms two
hydrogen bonds to residue Ile-50 and Ile-50^0 on two subunits
and another two hydrogen bonds to the inhibitor. Using the
HIV-1 protease as an example, this chapter illustrates the applica-
tion of WATsite with its PyMOL plugin for calculating the thermo-
dynamic profile of individual water molecules and their potential
contribution to ligand binding.2 Materials
2.1 Prerequisites The latest version of WATsite utilizes the OpenMM [15] toolkit for
GPU-accelerated molecular simulation. A GPU workstation is
required as well as OpenMM-WATsite, AmberTools16 [16], and
PyMOL [17].
2.2 Installation The WATsite3.0 package can be downloaded fromhttp://people.
pharmacy.purdue.edu/~mlill/software/watsite/version3.shtml.
WATsite.tar.gzneeds to be extracted using “tar –zxf WATsite.tar.
gz”. The fileWATsite_Settings.txtneeds to be copied to your home
Fig. 1Example of bound water in HIV-1 protease. Residues Ile-50 and Ile-50^0
from two subunits are shown in grey sticks, and inhibitor KNI in green sticks.
Water 301 is shown as red sphere, and yellow dashed lines represent hydrogen
bonds (PDB ID: 1hpx)390 Ying Yang et al.