RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
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DOI：
10.1002/pro.8
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发表时间：
2009-01-01
期刊：
影响因子：
8
通讯作者：
Baker, David
中科院分区：
文献类型：
--
作者：
Sheffler, Will;Baker, David
我们提出了一种称为RosettaHoles的新方法，用于蛋白质核心中的欠包装的视觉和定量评估。RosettaHoles生成一组球形空腔球，填充蛋白质内部原子之间的空体积。为了可视化，空腔球被聚集成连续的重叠簇，并且小的空腔被丢弃，留下结构中未填充的空间区域的整洁表示。对于定量分析，腔球数据用于估计在高分辨率晶体结构中观察到给定腔的概率。RosettaHoles在真实的和计算生成的结构之间提供了出色的区分，可以预测模型中的不正确区域，识别蛋白质数据库中有问题的结构，并有望成为新解决的实验结构的有用验证工具。
We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.