Li Zheng, Lazaridis Themis
Department of Chemistry, City College of New York, New York, NY, USA.
Methods Mol Biol. 2012;819:393-404. doi: 10.1007/978-1-61779-465-0_24.
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.
生物分子复合物结合界面处的水分子或从疏水腔中被置换出的水分子，近来已被视作结合亲和力的重要调节剂。计算这些水分子对溶剂化热力学贡献的一种方法是非均匀流体溶剂化理论（IFST）。在过去几年中，这种方法已应用于单个及成簇的界面水分子。我们对IFST的实现产生了有序水溶剂化热力学计算软件包（STOW）。本章概述了该理论及其应用，并描述了如何使用STOW计算有序水分子的热力学贡献。
