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

Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...

You might also read

Related Articles

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

Sort by
Same author

Engineering Symbiotic Nitrogen Fixation for Agriculture: Predominant Role of Host Plants and Fine-Tuning Regulation.

Plants (Basel, Switzerland)·2026
Same author

DNA Data Storage Architecture via Ligation of Dynamic DNA Bytes.

Small methods·2026
Same author

Structural insights into insect-selective sodium channel toxins drive AI-enhanced biopesticide design.

Nature communications·2026
Same author

Immunogenicity and Safety of Two-dose Schedules With Different Intervals of an ORF7-deficient Live Vaccine Candidate for Varicella: A Randomized, Double-blind, Controlled, Phase 2b Trial.

The Pediatric infectious disease journal·2026
Same author

<i>iMeta</i> Conference 2025: Creating high-impact international journals.

iMeta·2025
Same author

Metagenomics reveals potential interactions between Patescibacteriota and their phages in groundwater ecosystems.

mSystems·2025

Related Experiment Video

Updated: Jul 4, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

FragQA: predicting local fragment quality of a sequence-structure alignment.

Xin Gao1, Dongbo Bu, Shuai Cheng Li

  • 1David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada, N2L 3G1. x4gao@cs.uwaterloo.ca

Genome Informatics. International Conference on Genome Informatics
|June 12, 2008
PubMed
Summary

FragQA accurately predicts local protein model quality using sequence-structure alignments. This novel technique outperforms existing methods, aiding the structure biology community in refining protein models.

More Related Videos

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

Related Experiment Videos

Last Updated: Jul 4, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Protein structure prediction methods generate models with inherent errors.
  • Evaluating and refining these models is crucial for the structure biology community.
  • Identifying well- and poorly-predicted regions aids in model improvement.

Purpose of the Study:

  • To develop a novel technique for accurate local quality assessment of protein models.
  • To predict the quality of sequence-structure alignments from comparative modeling.
  • To identify specific regions within protein models that require refinement.

Main Methods:

  • Introduced FragQA, a novel technique for local quality prediction.
  • Utilized Support Vector Machines (SVM) regression for prediction.
  • Extracted information directly from sequence-structure alignments.

Main Results:

  • FragQA accurately predicts the local quality of sequence-structure alignments.
  • Achieved prediction accuracy superior to the top-performing method, ProQres.
  • Demonstrated that local sequence evolutionary information is a primary predictor.
  • Showed that structural features like solvent accessibility enhance prediction.

Conclusions:

  • Local protein model quality can be reliably predicted.
  • FragQA offers a valuable tool for assessing and refining protein models.
  • Sequence evolutionary information and structural features are key to accurate quality assessment.