COMPUTATION OF THE MEAN RESIDENCE TIME OF WATER IN THE HYDRATION SHELLS OF BIOMOLECULES
COMPUTATION OF THE MEAN RESIDENCE TIME OF WATER IN THE HYDRATION SHELLS OF BIOMOLECULES
复制标题
DOI：
10.1002/jcc.540141116
复制
发表时间：
1993-11-01
影响因子：
3
通讯作者：
STILLER, L
中科院分区：
文献类型：
--
作者：
GARCIA, AE;STILLER, L
在计算生物分子中原子位周围水化壳层的时间松弛行为的背景下，提出了一种算法。我们报道了蛋白质Crambin中极性、疏水和带电基团的第一和第二水合壳的时间松弛行为的计算。蛋白质基团周围的水平均停留时间是从325-ps分子动力学模拟过程中采集的构型平均值获得的。使用并行前缀算子实现了平均松弛时间计算中的卷积。给出了作为线性变换的并行前缀算子的一个新的刻画，这一表述使我们能够将卷积分解为两个并行前缀运算的乘积。并行前缀运算在对数时间内实现。(C)1993年，John Wiley&Sons，Inc.
An algorithm is presented within the context of the calculation of the time-relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time-relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325-ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. (C) 1993 by John Wiley & Sons, Inc.