Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data
Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data
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DOI：
10.1006/jsbi.2000.4350
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发表时间：
2001-02-01
影响因子：
3
通讯作者：
Birmanns, S
中科院分区：
文献类型：
--
作者：
Wriggers, W;Birmanns, S
我们在这里描述了一组多分辨率可视化和对接程序，我们称之为Situs包。该软件包的开发是为了提供一种有效和强大的方法，用于将原子结构拟合到低分辨率数据中。当前版本专门针对单个分子的可视化和对接进行了优化。一个新的3D图形查看器，volslice3d，开发的软件包，提供一个身临其境的虚拟现实环境的测量和渲染体积数据集。单分子，刚体对接的精度进行了测试模拟（无噪声）低分辨率密度图。对于通常在电子显微镜图像重建中出现的接近20埃的空间分辨率，可以实现大约1埃的对接精度。形状匹配分数在所有10个试验案例中捕获了正确的解决方案，并且足够严格，可以在8个系统中产生唯一的匹配。新的例程开发的原子结构的形状偏离相应的低分辨率形状的灵活对接。对肌动蛋白和乳铁蛋白异构体的测试计算表明，柔性对接忠实地再现了构象差异，精度
We describe here a set of multiresolution visualization and docking procedures that we refer to as the Situs package. The package was developed to provide an efficient and robust method for the fitting of atomic structures into low-resolution data. The current release was optimized specifically for the visualization and docking of single molecules. A novel 3D graphics viewer, volslice3d, was developed for the package to provide an immersive virtual reality environment for measuring and rendering volumetric data sets. The precision of single-molecule, rigid-body docking was tested on simulated (noise-free) low-resolution density maps. For spatial resolutions near 20 Angstrom typically arising in electron microscopy image reconstructions, a docking precision on the order of 1 Angstrom can be achieved. The shape-matching score captured the correct solutions in all 10 trial cases and was sufficiently stringent to yield unique matches in 8 systems. Novel routines were developed for the flexible docking of atomic structures whose shape deviates from the corresponding low-resolution shape. Test calculations on isoforms of actin and lactoferrin demonstrate that the flexible docking faithfully reproduces conformational differences with a precision