Extracting hydration sites around proteins from explicit water simulations
Extracting hydration sites around proteins from explicit water simulations
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DOI：
10.1002/jcc.10074
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发表时间：
2002-07-15
影响因子：
3
通讯作者：
McCammon, JA
中科院分区：
文献类型：
--
作者：
Henchman, RH;McCammon, JA
两种新的方法进行评估，确定周围的蛋白质水化位点的位置，从计算机模拟。目前的方法从蛋白质框架中构建的水密度的峰值中提取水合位点。然而.水分子的动态性质、附近的蛋白质残基和蛋白质参照系作为一个整体倾向于模糊水密度，使得更难以分辨位点。为了更好地求解水的密度，引入了两种技术。第一种方法是从蛋白质框架中每个水分子的时间平均位置构建水密度，同时水保持在该平均位置的给定距离内。第二种技术是从仅附近残基的参考系中的每个水的时间平均位置构建水密度。从水的密度确定水化位点的标准进行检查。这两种技术被发现显着改善的细节，在水的密度和检测到的水合位点的数量。(C)2002 Wiley Periodicals，Inc.
Two new methods are assessed for determining the location of hydration sites around proteins from computer simulation. Current methods extract hydration sites from peaks in the water density constructed in the protein frame. However. the dynamic nature of the water molecules, the nearby protein residues, and the protein reference frame as a whole tend to smear out the water density, making it more difficult to resolve sites. Two techniques are introduced to better resolve the water density. The first is to construct the water density from the time-averaged position of each water molecule in the protein frame while the water remains within a given distance of this averaged position. The second technique is to construct the water density from the time-averaged position of each water in the reference frame only of the nearby residues. Criteria for determining hydration sites from the water density are examined. Both techniques are found to significantly improve the detail in the water density and the number of hydration sites detected. (C) 2002 Wiley Periodicals, Inc.