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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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Related Experiment Video

Updated: Feb 17, 2026

Single Particle Cryo-Electron Microscopy: From Sample to Structure
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Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.

Xusi Han1, Qing Wei2, Daisuke Kihara1,2

  • 1Department of Biological Sciences, Purdue University, West Lafayette, Indiana.

Current Protocols in Bioinformatics
|December 9, 2017
PubMed
Summary

New tools, 3D-SURFER and EM-SURFER, enable rapid protein structure similarity searches using 3D Zernike descriptors (3DZD). These methods efficiently compare protein structures in large databases like the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB).

Keywords:
3D Zernike descriptorselectron microscopy maplocal geometric featureprotein structure comparisonprotein surface comparison

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) are rapidly expanding with solved protein structures.
  • Conventional structure alignment methods are too slow for real-time searches across these large databases.
  • Efficient tools are needed for high-throughput protein structure comparison and analysis.

Purpose of the Study:

  • To develop and describe 3D-SURFER and EM-SURFER for rapid, real-time protein structure similarity searches.
  • To utilize 3D Zernike descriptors (3DZD) for efficient comparison of protein structures.
  • To enable analysis of local geometric features and interpretation of search results.

Main Methods:

  • Development of 3D-SURFER and EM-SURFER tools.
  • Computation of 3D Zernike descriptors (3DZD) for query proteins.
  • Comparison of query 3DZD against databases (PDB, EMDB).
  • Utilizing VisGrid and LIGSITECSC for local geometric analysis.

Main Results:

  • 3D-SURFER and EM-SURFER enable high-throughput protein structure comparison.
  • The tools facilitate real-time similarity searches against large structural databases.
  • Analysis of local geometric characteristics is integrated into the workflow.

Conclusions:

  • 3D-SURFER and EM-SURFER provide efficient solutions for protein structure similarity searches.
  • The use of 3D Zernike descriptors allows for rapid and scalable comparisons.
  • These tools enhance the analysis and visualization of protein structures.