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Related Concept Videos

Atomic Structure01:33

Atomic Structure

All matter is composed of atoms, the smallest individual units of elements. Each atom is made up of three subatomic particles: protons, neutrons, and electrons. Together, these three particles account for the mass and the charge of an atom.The History of Atomic TheoryThe first person to propose that everything on Earth is made up of tiny particles was the Greek philosopher Democritus, around 450 B.C. He used the term atomos, Greek for “indivisible,” from which the modern term “atom” is derived.
Atomic Structure01:17

Atomic Structure

The Greek philosopher Democritus proposed that everything on Earth is made up of tiny particles called atomos, Greek for "indivisible," from which the modern term "atom" is derived. In the 19th century, John Dalton proposed the atomic theory that is still largely correct today. He put forth five postulates to explain how atoms made up the world around us. (1) All matter is composed of infinitely small particles or atoms. (2) All atoms of a given element are identical to one another and (3) are...

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Related Experiment Video

Updated: Jun 28, 2026

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
08:16

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Published on: March 19, 2021

Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local

Yaxian Cai1, Ziying Zhang1, Xiangyu Xu1

  • 1College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China.

Journal of Chemical Information and Modeling
|March 28, 2025
PubMed
Summary

DEMO-EMfit accurately fits atomic structures into cryo-electron microscopy (cryo-EM) density maps. This new method improves upon existing techniques for structural fitting in cryo-EM and cryo-electron tomography (cryo-ET) data.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Accurate atomic model construction from cryo-electron microscopy (cryo-EM) density maps is crucial.
  • The precision of structure-to-map fitting directly impacts the quality of the final atomic models.

Purpose of the Study:

  • To introduce DEMO-EMfit, a novel progressive method for fitting atomic structures into cryo-EM density maps.
  • To enhance the accuracy and efficiency of atomic model building in cryo-EM and cryo-electron tomography (cryo-ET).

Main Methods:

  • DEMO-EMfit integrates deep learning-based backbone map extraction.
  • It employs a global-local structural pose search for precise fitting.
  • The method was validated on a diverse benchmark dataset.

Main Results:

  • DEMO-EMfit demonstrated superior performance compared to state-of-the-art methods.
  • The tool proved efficient and accurate across various cryo-EM and cryo-ET maps.
  • Successful fitting was achieved for protein and nucleic acid complexes.

Conclusions:

  • DEMO-EMfit offers a significant advancement in structural fitting for cryo-EM data.
  • The method provides a reliable and efficient solution for atomic model construction.
  • It is a valuable tool for researchers in structural biology and related fields.