AQUARIUS2 - KNOWLEDGE-BASED MODELING OF SOLVENT SITES AROUND PROTEINS
AQUARIUS2 - KNOWLEDGE-BASED MODELING OF SOLVENT SITES AROUND PROTEINS
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DOI：
10.1002/jcc.540140902
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发表时间：
1993-09-01
影响因子：
3
通讯作者：
GOODFELLOW, JM
中科院分区：
文献类型：
--
作者：
PITT, WR;MURRAYRUST, J;GOODFELLOW, JM
程序 AQUARIUS2 计算原子坐标已知的任何蛋白质的第一水合壳内水分子的可能位置。与它的前身 AQUARIUS 一样，它利用了晶体学确定的蛋白质结构中的水分子位点知识。不采用能量计算。它与原始程序的显着不同在于，在蛋白质表面周围生成 3D 概率图（针对溶剂位点），而不是先前使用的离散点。该程序的准确性是通过与程序知识库中未使用的蛋白质的实验得出的水分子位置进行比较来衡量的。还通过将蛋白质胆色素原脱氨酶的概率密度图与晶体学确定的电子密度图相结合来对其进行了测试。该程序从背景噪声中过滤出最可能的溶剂电子密度峰，并已用于确定蛋白质神经生长因子周围的溶剂结构。 (C) 1993 年，约翰·威利父子公司 (John Wiley & Sons, Inc.)
The program AQUARIUS2 calculates probable positions for water molecules within the first hydration shell of any protein for which atomic coordinates are known. Like its predecessor, AQUARIUS, it uses a knowledge of water molecules sites from crystallographically determined protein structures. Energy calculations are not employed. It differs substantially from the original program in that a 3-D probability map (for solvent sites) is generated around the surface of the protein instead of the previously used discrete points. The accuracy of the program has been gauged by comparison with experimentally derived water molecule positions for proteins not used in the knowledge base of the program. It has also been tested by combining the probability density maps with crystallographically determined electron density maps for the protein porphobilinogen deaminase. This procedure filters the most likely solvent electron density peaks from the background noise and has been used in the determination of the solvent structure around the protein nerve growth factor. (C) 1993 by John Wiley & Sons, Inc.