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

Protein Folding

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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...

You might also read

Related Articles

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

Sort by

Same author

Macrophages restrict tumor immune infiltration by controlling collagen topography.

Science immunology·2026

Same author

Semi-supervised segmentation of RNA 3D structures using density-based clustering.

Computational and structural biotechnology journal·2026

Same author

RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.

Scientific reports·2025

Same author

Beyond classical domains: The protein unit paradigm - from protein-architecture characterization to downstream applications.

Biochimie·2025

Same author

Flexibility or uncertainty? A critical assessment of AlphaFold 2 pLDDT.

Structure (London, England : 1993)·2025

Same author

Using protein blocks to build custom fragment libraries from protein structures.

Biochimie·2025

Search research articles

Related Experiment Video

Updated: Apr 5, 2026

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

Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.

Yassine Ghouzam¹, Guillaume Postic¹, Alexandre G de Brevern¹

¹Inserm U1134, Paris, France, Université Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France, Institut National de la Transfusion Sanguine, Paris, France and Laboratory of Excellence GR-Ex, Paris, France.

Bioinformatics (Oxford, England)

|August 9, 2015

Summary

This summary is machine-generated.

ORION, a novel fold recognition method, enhances protein 3D structure prediction by integrating sequence and structural information. This approach improves the detection of evolutionary relationships, outperforming existing tools.

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Apr 5, 2026

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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Template-based modeling is crucial for protein 3D structure prediction.
Detecting distant evolutionary relationships is key for homology detection.
Current methods primarily use evolutionary information from amino acid sequences.

Purpose of the Study:

To introduce ORION, a new fold recognition method.
To improve the detection of remote homology in protein sequences.
To enhance protein structure prediction by incorporating structural information.

Main Methods:

ORION utilizes pairwise comparison of hybrid profiles.
Hybrid profiles combine evolutionary information from protein sequence and structure.
The method employs the 16-state structural alphabet, Protein Blocks, for local conformation description.

Main Results:

ORION outperforms PSI-BLAST and HHsearch on multiple benchmarks.
The method demonstrates superior performance on CASP8, 9, and 10 target sequences.
ORION detects approximately 10% more templates at fold and superfamily SCOP levels.

Conclusions:

ORION represents a significant advancement in fold recognition.
Integrating sequence and structural information improves homology detection.
The method enhances the accuracy of protein 3D structure prediction.