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Updated: Mar 1, 2026

Cryo-EM and Single-Particle Analysis with Scipion

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Published on: May 29, 2021

EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy

Niyun Zhou^1,2, Hongwei Wang^3,4, Jiawei Wang⁵

¹MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China.

Scientific Reports

|June 3, 2017

Summary

This summary is machine-generated.

A new program, EMBuilder, automates de novo cryo-electron microscopy (cryoEM) model building for high-resolution maps. It efficiently generates protein models, reducing manual labor for structural biologists.

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Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Single-particle cryo-electron microscopy (cryoEM) is achieving near-atomic resolution.
De novo model building in cryoEM maps beyond 3.5 Å resolution is currently challenging.
Automated tools are needed to streamline the interpretation of high-resolution cryoEM data.

Purpose of the Study:

To develop a novel computational program for de novo model building in high-resolution cryoEM maps.
To enable automated generation of protein structural models from electron-potential maps.
To reduce the manual workload and time associated with cryoEM model building.

Main Methods:

EMBuilder utilizes template matching for identifying secondary structure elements (helices and strands).
The program refines voxel size to correct for magnification errors.
It employs a log-likelihood (LLK) target function to extend secondary structures and assign side chains.

Main Results:

EMBuilder successfully builds models for large proteins (up to ~1 MDa).
The program completes model building within approximately one day.
It demonstrates potential for accurate de novo model generation at high resolutions.

Conclusions:

EMBuilder offers an automated solution for de novo model building in high-resolution cryoEM.
The program significantly reduces the manual effort required for interpreting cryoEM maps.
This tool has the potential to accelerate structural determination using cryoEM.