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

Automatic Processing and Automatic Social Behavior01:28

Automatic Processing and Automatic Social Behavior

253
Automatic processing refers to the cognitive operations that occur without conscious intent or awareness, playing a fundamental role in shaping social cognition and behavior. These processes enable individuals to navigate complex social environments efficiently by relying on mental shortcuts and pre-existing knowledge structures known as schemas. One of the most influential mechanisms underlying automatic processing is priming, which subtly activates mental representations through exposure to...
253
Systematic Error: Methodological and Sampling Errors01:15

Systematic Error: Methodological and Sampling Errors

11.0K
In the case of systematic errors, the sources can be identified, and the errors can be subsequently minimized by addressing these sources. According to the source, systematic errors can be divided into sampling, instrumental, methodological, and personal errors.
Sampling errors originate from improper sampling methods or the wrong sample population. These errors can be minimized by refining the sampling strategy. Defective instruments or faulty calibrations are the sources of instrumental...
11.0K
Fundamental Attribution Error01:14

Fundamental Attribution Error

13.8K
According to some social psychologists, people tend to overemphasize internal factors as explanations—or attributions—for the behavior of other people. They tend to assume that the behavior of another person is a trait of that person, and to underestimate the power of the situation on the behavior of others. They tend to fail to recognize when the behavior of another is due to situational variables, and thus to the person’s state. This erroneous assumption is...
13.8K
Matrix Proteoglycans and Glycoproteins01:21

Matrix Proteoglycans and Glycoproteins

5.1K
Proteoglycans are extensively glycosylated proteins, commonly found in the extracellular matrix, interwoven with collagen fibers. Hyaline cartilage, the most common type of cartilage in the body, consists of short and dispersed collagen fibers associated with large amounts of proteoglycans. These proteoglycans have long negative charges that attract cations, which in turn attract water molecules. This influx of ions and water molecules swells up the proteoglycan like a water-soaked gel that can...
5.1K
Random Error01:04

Random Error

9.8K
Random or indeterminate errors originate from various uncontrollable variables, such as variations in environmental conditions, instrument imperfections, or the inherent variability of the phenomena being measured. Usually, these errors cannot be predicted, estimated, or characterized because their direction and magnitude often vary in magnitude and direction even during consecutive measurements. As a result, they are difficult to eliminate. However, the aggregate effect of these errors can be...
9.8K
Margin of Error01:27

Margin of Error

7.6K
The margin of error is also called the maximum error of an estimate. The margin of error is the maximum possible or expected difference between the observed sample parameter value and the actual population parameter value. For proportion, it is the maximum difference between the value of sample proportion obtained from the data and the true value of population proportion. As the true value of the population parameter is not known, the margin of error is calculated using the sample statistic.
7.6K

You might also read

Related Articles

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

Sort by
Same author

Controlling metal-carbonate phase, form, and function through de novo protein design.

bioRxiv : the preprint server for biology·2026
Same author

Author Correction: De novo design of quasisymmetric two-component protein cages.

Nature·2026
Same author

De novo design of quasisymmetric two-component protein cages.

Nature·2026
Same author

Design of one-component quasisymmetric protein nanocages.

Nature·2026
Same author

Redesign of TALE proteins for DNA-templated assembly of protein fibers.

Nature communications·2026
Same author

Mutations to the HCoV-229E spike have counterbalancing effects on serum antibody neutralization and receptor binding.

bioRxiv : the preprint server for biology·2026
Same journal

Cryo-EM structure of the Arabidopsisthaliana ribosome in translating and non-translating states.

Structure (London, England : 1993)·2026
Same journal

Multifaceted effects of N-glycosylation on amyloidogenic κ light chains in AL amyloidosis.

Structure (London, England : 1993)·2026
Same journal

Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome.

Structure (London, England : 1993)·2026
Same journal

Saxiphilin is a broad-spectrum toxin sponge for C13-modified saxitoxins.

Structure (London, England : 1993)·2026
Same journal

Cryo-EM structure of YfdQ reveals a widespread family of bacteriophage-associated proteins with shell-like assemblies.

Structure (London, England : 1993)·2026
Same journal

An extracellular allosteric gate modulates the ligand efficacy of GPR119.

Structure (London, England : 1993)·2026
See all related articles

Related Experiment Video

Updated: Feb 3, 2026

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging
07:29

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

Published on: December 1, 2011

42.0K

Automatically Fixing Errors in Glycoprotein Structures with Rosetta.

Brandon Frenz1, Sebastian Rämisch2, Andrew J Borst3

  • 1Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.

Structure (London, England : 1993)
|October 23, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a new Rosetta-based method to fix errors in carbohydrate structures within glycoproteins, improving accuracy for both cryo-electron microscopy (cryoEM) and X-ray crystallography. The approach enhances glycan geometry refinement in deposited protein structures.

Keywords:
cryoEMglycansglycoproteinsrefinement

More Related Videos

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo
08:29

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Published on: October 21, 2014

12.6K
Automatic Image Processing to Determine the Community Size Structure of Riverine Macroinvertebrates
08:56

Automatic Image Processing to Determine the Community Size Structure of Riverine Macroinvertebrates

Published on: January 13, 2023

2.9K

Related Experiment Videos

Last Updated: Feb 3, 2026

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging
07:29

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

Published on: December 1, 2011

42.0K
Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo
08:29

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Published on: October 21, 2014

12.6K
Automatic Image Processing to Determine the Community Size Structure of Riverine Macroinvertebrates
08:56

Automatic Image Processing to Determine the Community Size Structure of Riverine Macroinvertebrates

Published on: January 13, 2023

2.9K

Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Single-particle cryo-electron microscopy (cryoEM) advances enable protein structure determination with resolved glycans.
  • Existing refinement protocols struggle with low-resolution glycoprotein structures, leading to glycan stereochemical errors in deposited data.

Purpose of the Study:

  • To develop and validate a Rosetta-based computational approach for refining glycoproteins.
  • To correct conformational and configurational errors in carbohydrate moieties within protein structures.

Main Methods:

  • A modified Rosetta framework incorporating new features and score terms for automatic glycan detection and refinement.
  • Benchmarking the approach using 12 crystal structures to assess improvements in glycan geometry.
  • Application to human coronavirus NL63 spike glycoprotein and an HIV envelope glycoprotein.

Main Results:

  • The Rosetta-based method successfully corrects glycan stereochemical errors.
  • Automated refinement improves glycan geometries while maintaining good fit to crystallographic data.
  • Demonstrated utility for cryoEM refinement of complex glycoproteins.

Conclusions:

  • The developed Rosetta approach offers a robust solution for accurate glycoprotein refinement.
  • This method addresses a critical limitation in current structural biology workflows.
  • Enables more reliable structural data deposition and interpretation for glycoproteins.