Navigating 3D electron microscopy maps with EM-SURFER

BMC Bioinformatics

Daisuke Kihara³  Charles Christoffer¹  Shuomeng Guang³  Xusi Han³  Yi Xiong³  Juan Esquivel-Rodríguez² 

[1]Department of Mathematics, Purdue University, West Lafayette 47907, IN, USA

[2]Department of Computer Science, Purdue University, West Lafayette 47907, IN, USA

[3]Department of Biological Sciences, Purdue University, West Lafayette 47907, IN, USA

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

Others  :  1232219
DOI  :  10.1186/s12859-015-0580-6

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

【 摘 要 】

Background

The 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.

Results

We 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.

Conclusions

We 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】

   
2015 Esquivel-Rodriguez et al.; licensee BioMed Central.

【 图 表 】

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