Han Xusi, Wei Qing, Kihara Daisuke
Department of Biological Sciences, Purdue University, West Lafayette, Indiana.
Department of Computer Science, Purdue University, West Lafayette, Indiana.
Curr Protoc Bioinformatics. 2017 Dec 8;60:3.14.1-3.14.15. doi: 10.1002/cpbi.37.
With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE in 3D-SURFER. This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc.
随着蛋白质数据库（PDB）和电子显微镜数据库（EMDB）中已解析蛋白质结构数量的迅速增长，开发能够针对整个结构数据库进行实时结构相似性搜索的工具至关重要。由于传统的结构比对方法需要在三维空间中对蛋白质的不同取向进行采样，它们耗时且不适用于快速的实时数据库搜索。为此，我们开发了3D-SURFER和EM-SURFER，它们利用三维泽尼克描述符（3DZD）进行高通量蛋白质结构比较、可视化和分析。以蛋白质或蛋白质复合物的原子结构或电子显微镜图谱作为输入，计算查询蛋白质的3DZD，并将其与PDB或EMDB中所有其他蛋白质的3DZD进行比较。此外，可在3D-SURFER中使用VisGrid和LIGSITE分析查询蛋白质的局部几何特征。本文介绍了如何使用3D-SURFER和EM-SURFER进行蛋白质表面形状相似性搜索、局部几何特征分析以及搜索结果的解读。© 2017约翰威立父子出版公司
