Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 Stadium Mall Drive , West Lafayette , Indiana 47906 , United States.
J Chem Inf Model. 2018 Nov 26;58(11):2183-2188. doi: 10.1021/acs.jcim.8b00544. Epub 2018 Oct 24.
Molecular dynamics (MD) simulations allow for accurate prediction of the thermodynamic profile of binding-site water molecules critical for protein-ligand association. Whereas this hydration-site profiling converges rapidly for solvent-exposed sites independent of the initial water placement, an accurate and reliable placement is required for water molecules in occluded binding sites. Here, we present an accurate and efficient hydration-site prediction method for occluded binding sites combining water placement based on 3D-RISM and MD simulations using WATsite.
分子动力学（MD）模拟可以准确预测对蛋白质-配体结合至关重要的结合位点水分子的热力学分布。虽然对于暴露于溶剂的位点，溶剂化位点分析可以快速收敛，而与初始水分子位置无关，但对于被掩蔽结合位点中的水分子，则需要准确和可靠的位置。在这里，我们提出了一种结合 3D-RISM 基于水分子位置的方法和 WATsite 进行 MD 模拟的准确高效的掩蔽结合位点水合位点预测方法。
