Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

2.7K
Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
2.7K
¹H NMR Signal Multiplicity: Splitting Patterns01:13

¹H NMR Signal Multiplicity: Splitting Patterns

6.4K
When protons A and X are coupled, their nuclear spin energy levels are slightly modified. This is because the energy required to excite proton A to a spin state parallel to proton X is slightly different from the energy required for it to become anti-parallel to spin X. Consequently, there are two possible excitation frequencies for A (A1 and A2), depending on the spin state of X, and vice versa. The mutual nature of coupling implies that the difference between frequencies A1 and A2, indicated...
6.4K
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

2.3K
In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the...
2.3K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Crystalline 3D covalent organic frameworks with nbo topology.

Science advances·2026
Same author

Crystal structure determination of an Fe<sup>II</sup> azo aldehyde complex [Fe(C<sub>14</sub>H<sub>11</sub>N<sub>2</sub>O<sub>3</sub>)<sub>2</sub>(H<sub>2</sub>O)<sub>2</sub>] by MicroED.

Acta crystallographica. Section E, Crystallographic communications·2026
Same author

Structure of the bacteriophage PhiKZ non-virion RNA polymerase bound to a p119L open promoter analogue.

IUCrJ·2025
Same author

Reversible and Massive Structural Transformation in Meltable Cyanido-bridged Coordination Polymer Crystals.

Chemistry (Weinheim an der Bergstrasse, Germany)·2025
Same author

Beyond serendipity: uncovering novel ratiometric urea·24DHBA cocrystals through mechanochemistry and MicroED.

Chemical communications (Cambridge, England)·2025
Same author

Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization.

Cell·2025

Related Experiment Video

Updated: Dec 18, 2025

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
13:28

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

50.7K

Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER.

Kailash Ramlaul1, Colin M Palmer2, Takanori Nakane3

  • 1Section for Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College Road, South Kensington, London SW7 2BB, United Kingdom.

Journal of Structural Biology
|June 14, 2020
PubMed
Summary

Over-fitting in single particle analysis can corrupt structural biology results. A new SIDESPLITTER method reduces noise-induced over-fitting, improving structural accuracy, especially for challenging small proteins.

Keywords:
Cryo-EMLocal resolutionNoise suppressionOver-fittingReal-space filter

More Related Videos

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency
06:41

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Published on: May 10, 2024

2.4K
Cryo-EM and Single-Particle Analysis with Scipion
09:06

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

4.3K

Related Experiment Videos

Last Updated: Dec 18, 2025

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
13:28

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Published on: May 16, 2017

50.7K
Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency
06:41

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Published on: May 10, 2024

2.4K
Cryo-EM and Single-Particle Analysis with Scipion
09:06

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

4.3K

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Single particle analysis is crucial for determining molecular structures.
  • Experimental data often suffers from high noise levels, leading to over-fitting during reconstruction.
  • Over-fitting can result in inaccurate structural interpretations and flawed biological conclusions.

Purpose of the Study:

  • To address persistent over-fitting issues in single particle analysis, particularly in low signal-to-noise regions.
  • To introduce and validate a novel refinement strategy to mitigate over-fitting.
  • To improve the accuracy and resolution of cryo-electron microscopy reconstructions.

Main Methods:

  • Development of SIDESPLITTER, a local signal-to-noise filtering approach for refinement.
  • Application of SIDESPLITTER to both idealized and experimental single particle analysis datasets.
  • Independent refinement of split datasets with and without the SIDESPLITTER modification.

Main Results:

  • SIDESPLITTER effectively reduces over-fitting, even in low signal-to-noise areas.
  • The method maintains the independence of split datasets during refinement.
  • Improved density maps and enhanced resolution were observed, particularly for small membrane proteins.

Conclusions:

  • SIDESPLITTER offers a robust solution to over-fitting in single particle analysis.
  • The technique enhances structural accuracy and reliability of cryo-EM reconstructions.
  • This method is particularly beneficial for challenging datasets, such as small proteins and membrane proteins.