Computing the thermodynamic contributions of interfacial water.

Water molecules at the binding interface of biomolecular complexes or water molecules displaced from hydrophobic cavities have lately been recognized as important modulators of binding affinity. One approach to computing the contribution of these water molecules to solvation thermodynamics is inhomogeneous fluid solvation theory (IFST). Over the past few years this approach has been applied to interfacial water molecules, both individual and in clusters. Our implementation of IFST resulted in the computational package Solvation Thermodynamics of Ordered Water (STOW). This chapter gives an overview of the theory and its applications and describes how to calculate the thermodynamic contributions of ordered water molecules using STOW.