Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Folding Quality Check in the RER

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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Folding

Protein Folding

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

You might also read

Related Articles

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

Sort by

Same author

De novo design of epitope-specific antibodies via a structure-driven computational workflow.

Nature communications·2025

Same author

Using Large Language Models for Chronic Disease Management Tasks: Scoping Review.

JMIR medical informatics·2025

Same author

14-3-3/HIP-55 complex attenuates cardiomyocyte apoptosis.

Journal of molecular and cellular cardiology·2025

Same author

Seedlings of rye (<i>Secale cereale</i>) respond to freeze-thaw, alkaline salt, and <i>Solanum rostratum</i> Dunal extract combined stress by increasing soluble protein and antioxidant enzyme activity.

Functional plant biology : FPB·2025

Same author

Pollution characteristics, distribution and risk level of heavy metals in sediments of the Yangtze River estuary.

Heliyon·2024

Same author

Prediction of risk factors of sleep disturbance in patients undergoing total hip arthroplasty.

Sleep and biological rhythms·2024

Same journal

Model-based quantification of protein-protein interaction aberrations for exploring dysregulated signalling pathways through pathway maps and gene expression levels.

BMC bioinformatics·2026

Same journal

Research on multi-trait genome association study method based on Shannon information entropy.

BMC bioinformatics·2026

Same journal

A multi-view feature fusion framework with interpretable graph convolution for predicting microbe-drug associations.

BMC bioinformatics·2026

Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026

Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026

Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 23, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

A single-model quality assessment method for poor quality protein structure.

Jianquan Ouyang¹, Ningqiao Huang², Yunqi Jiang³

¹key Laboratory of Intelligent Computing & Information Processing, Ministry of Education, Xiangtan University, Xiangtan, China. 27894827@qq.com.

BMC Bioinformatics

|April 27, 2020

Summary

This summary is machine-generated.

A new method accurately assesses protein structure model quality using six features, outperforming existing techniques for low-quality models. This approach aids in selecting reliable protein structures from large, diverse datasets.

Keywords:

Linear combination Poor quality protein structural Protein model quality assessment Protein structure ranking

More Related Videos

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Published on: December 30, 2016

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: Dec 23, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Published on: December 30, 2016

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Assessing protein tertiary structure model quality is vital for determining model utility.
Selecting high-quality protein models from decoys is a significant challenge.
Current methods lack consensus for selecting good models from poor-quality pools.

Purpose of the Study:

To develop a novel single-model quality assessment method for low-quality protein models.
To improve the accuracy of selecting reliable protein structures from large datasets.

Main Methods:

Utilized a simple linear combination of six features for quality assessment.
Employed weighted search and linear regression on a large dataset.
Benchmarked performance on models from the Critical Assessment of Protein Structure Prediction (CASP12 and CASP13).

Main Results:

The novel method demonstrates outstanding performance specifically on poor-quality protein models.
Achieved high accuracy in quality assessment for protein structure prediction.
Validated the method's effectiveness on independent datasets.

Conclusions:

Quality assessment of protein structures can be improved using a limited set of predictive features.
Contact prediction is a key feature for enhancing selection accuracy.
The proposed method offers a robust approach for evaluating protein model quality.