Baker Matthew L, Ju Tao, Chiu Wah
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Structure. 2007 Jan;15(1):7-19. doi: 10.1016/j.str.2006.11.008.
An increasing number of structural studies of large macromolecular complexes, both in X-ray crystallography and cryo-electron microscopy, have resulted in intermediate-resolution (5-10 A) density maps. Despite being limited in resolution, significant structural and functional information may be extractable from these maps. To aid in the analysis and annotation of these complexes, we have developed SSEhunter, a tool for the quantitative detection of alpha helices and beta sheets. Based on density skeletonization, local geometry calculations, and a template-based search, SSEhunter has been tested and validated on a variety of simulated and authentic subnanometer-resolution density maps. The result is a robust, user-friendly approach that allows users to quickly visualize, assess, and annotate intermediate-resolution density maps. Beyond secondary structure element identification, the skeletonization algorithm in SSEhunter provides secondary structure topology, which is potentially useful in leading to structural models of individual molecular components directly from the density.
在X射线晶体学和冷冻电子显微镜领域，越来越多针对大型大分子复合物的结构研究已生成中等分辨率（5-10埃）的密度图。尽管分辨率有限，但仍可从这些图中提取重要的结构和功能信息。为了辅助对这些复合物进行分析和注释，我们开发了SSEhunter，这是一种用于定量检测α螺旋和β折叠的工具。基于密度骨架化、局部几何计算以及基于模板的搜索，SSEhunter已在各种模拟和真实的亚纳米分辨率密度图上进行了测试和验证。结果是一种强大且用户友好的方法，允许用户快速可视化、评估和注释中等分辨率密度图。除了二级结构元件识别之外，SSEhunter中的骨架化算法还提供二级结构拓扑，这可能有助于直接从密度得出单个分子组件的结构模型。
