Cheng Anchi, Yeager Mark
The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
J Struct Biol. 2007 Apr;158(1):19-32. doi: 10.1016/j.jsb.2006.10.003. Epub 2006 Oct 20.
Difference density maps are commonly used in structural biology for identifying conformational changes in macromolecular complexes. For interpretation of the results, it is essential to estimate the variance or standard deviation of the difference density and the distribution of errors in space. In order to compare three-dimensional density maps of gap junction channels with and without the C-terminal regulatory domain, we developed a bootstrap resampling method for estimation of the voxel-wise standard deviation. The bootstrap approach has been successfully used for estimating the sampling distribution from a limited data set and for estimating the statistical properties of the derived quantities [Efron, B., 1979. Bootstrap methods: another look at the jackknife. Ann. Stat. 7, 1-26]. In our application, the standard deviation map can be estimated by bootstrapping the images. Our results show that, apart from the symmetry axes and small regions bordering the lumen of the extracellular vestibule, difference maps normalized by the mean of the standard deviation map can be used as a good approximation of the t-test map of the gap junction crystals.
差异密度图在结构生物学中常用于识别大分子复合物的构象变化。为了解释结果，估计差异密度的方差或标准差以及空间中误差的分布至关重要。为了比较有和没有C端调节域的间隙连接通道的三维密度图，我们开发了一种用于估计体素级标准差的自助重采样方法。自助法已成功用于从有限的数据集中估计采样分布以及估计派生量的统计特性[Efron, B., 1979. 自助法：对刀切法的再审视。《统计学年鉴》7, 1 - 26]。在我们的应用中，标准差图可以通过对图像进行自助抽样来估计。我们的结果表明，除了对称轴和与细胞外前庭腔相邻的小区域外，用标准差图的均值归一化后的差异图可以很好地近似间隙连接晶体的t检验图。
