Navigating 3D electron microscopy maps with EM-SURFER

BMC Bioinformatics

Software

Xusi Han¹  Shuomeng Guang¹  Yi Xiong¹  Juan Esquivel-Rodríguez²  Daisuke Kihara³  Charles Christoffer⁴ 

[1] Department of Biological Sciences, Purdue University, 47907, West Lafayette, IN, USA;Department of Computer Science, Purdue University, 47907, West Lafayette, IN, USA;Department of Computer Science, Purdue University, 47907, West Lafayette, IN, USA;Department of Biological Sciences, Purdue University, 47907, West Lafayette, IN, USA;Department of Computer Science, Purdue University, 47907, West Lafayette, IN, USA;Department of Mathematics, Purdue University, 47907, West Lafayette, IN, USA;

关键词: Electron microscopy;    Electron density maps;    EM Data Bank;    EMDB;    3D Zernike Descriptors;    Proteins;    Macromolecular structure;    Low-resolution structure data;    Database search;   

DOI  :  10.1186/s12859-015-0580-6

 received in 2014-07-24, accepted in 2015-04-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established.ResultsWe developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed.ConclusionsWe developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.

【 授权许可】

Unknown   
© Esquivel-Rodriguez et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.