蛋白质构象空间的汉明距离几何。应用于HIV-1整合酶催化核心的4 ns分子动力学轨迹的聚类
Hamming distance geometry of a protein conformational space. Application to the clustering of a 4 ns molecular dynamics trajectory of the HIV-1 integrase catalytic core
摘要：
蛋白质结构可以被编码成二进制序列，这些序列用于定义构象空间中的汉明距离：两个不同分子构象之间的距离是它们序列中不同位的数量。序列中的每一位都来自于构象空间的两半划分。因此，编码在二进制序列中的信息也用于表征系统访问的构象空间的区域。我们应用这个距离和它们相关的几何结构，聚类和分析的构象采样期间的4 ns分子动力学模拟的HIV-1整合酶催化核心。模拟的聚类分析表明，轨迹分为两个部分的2.6和1.4纳秒的长度，这是定性不同的：数据点的事实，平衡只达到在第一段结束。一些长度的文件是专门比较汉明距离的r.m.s.偏差测量对迄今为止研究的案例的分析表明，在相同条件下，这两种度量表现得非常不同，并且汉明距离似乎比r.m.s.偏差
英文摘要：
Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space in two halves. Thus, the information encoded in the binary sequences is also used to characterize the regions of conformational space visited by the system. We apply this distance and their associated geometric structures, to the clustering and analysis of conformations sampled during a 4 ns molecular dynamics simulation of the HIV-1 integrase catalytic core. The cluster analysis of the simulation shows a division of the trajectory into two segments of 2.6 and 1.4 ns length, which are qualitatively different: the data points to the fact that equilibration is only reached at the end of the first segment. Some length of the paper is devoted to compare the Hamming distance to the r.m.s. deviation measure. The analysis of the cases studied so far, shows that under the same conditions the two measures behave quite differently, and that the Hamming distance appears to be more robust than the r.m.s. deviation.
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