Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
BMC Bioinformatics. 2010 Dec 14;11 Suppl 11(Suppl 11):S2. doi: 10.1186/1471-2105-11-S11-S2.
Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed.
The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification.
Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.
用于确定蛋白质三级结构的实验技术的最新进展给蛋白质生物信息学带来了重大挑战。随着未知功能结构数量的快速增长，急需大规模提供其生物学功能的可靠线索。由于速度较慢，传统的结构比较方法不适合实时数据库搜索。此外，最近的技术（如电子显微镜（EM））带来了新的挑战，因为这些技术提供的是低分辨率的结构数据。之前，我们已经介绍了一种使用 3D Zernike 描述符（3DZD）表示蛋白质表面形状的方法。3DZD 利用其旋转不变性和紧凑表示，实现了快速的结构数据库搜索。使用 3DZD 表示的蛋白质表面的搜索结果与现有的结构分类具有良好的一致性，但也观察到了一些差异。
本文研究了三种新的骨架原子表面表示方法，包括原始的全原子表面表示方法、全原子表面与骨架表示的组合。所有表示方法都使用 3DZD 进行编码。此外，我们还研究了 3DZD 用于搜索不同分辨率的蛋白质 EM 密度图的适用性。使用两种现有的分类（SCOP 和基于 CE 的分类）对表面表示进行了结构检索评估。
总体而言，代表骨架原子的 3DZD 比原始的全原子表面表示具有更好的检索性能。当两种表示方法结合使用时，性能进一步提高。此外，我们还观察到 3DZD 对于比较电子显微镜获得的低分辨率结构也非常有效。
