Institute of Complex Systems, Forschungszentrum Jülich, Jülich, Germany.
Biopolymers. 2012 Sep;97(9):687-97. doi: 10.1002/bip.22046.
Single-particle cryo-electron microscopy (cryo-EM) has become an important tool to determine the structure of large biomolecules and assemblies thereof. However, the achievable resolution varies considerably over a wide range of about 3.5-20 Å. The interpretation of these intermediate- to low-resolution density maps in terms of atomic models is a big challenge and an area of active research. Here, we present our real-space structure refinement program DireX, which was developed primarily for cryo-EM-derived density maps. The basic principle and its main features are described. DireX employs Deformable Elastic Network (DEN) restraints to reduce overfitting by decreasing the effective number of degrees of freedom used in the refinement. Missing or reduced density due to flexible parts of the protein can lead to artifacts in the structure refinement, which is addressed through the concept of restrained grouped occupancy refinement. Furthermore, we describe the performance of DireX in the 2010 Cryo-EM Modeling Challenge, where we chose six density maps of four different proteins provided by the Modeling Challenge exemplifying typical refinement results at a large resolution range from 3 to 23 Å.
单颗粒冷冻电子显微镜（cryo-EM）已成为确定大型生物分子及其组装体结构的重要工具。然而，在大约 3.5-20 Å 的广泛范围内，可达到的分辨率差异很大。根据原子模型解释这些中-低分辨率密度图是一个巨大的挑战，也是一个活跃的研究领域。在这里，我们介绍了我们的直接空间结构精修程序 DireX，该程序主要是为 cryo-EM 衍生的密度图开发的。描述了其基本原理和主要特点。DireX 使用可变形弹性网络（DEN）约束来减少过度拟合，从而减少精修中使用的有效自由度数量。由于蛋白质的柔性部分导致的缺失或减少的密度可能会导致结构精修中的伪影，通过受限分组占有率精修的概念来解决这个问题。此外，我们还描述了 DireX 在 2010 年 cryo-EM 建模挑战赛中的表现，我们选择了挑战赛提供的四个不同蛋白质的六个密度图，这些密度图代表了从 3 到 23 Å 的大分辨率范围内的典型精修结果。
