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 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 can...

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 Organization

Protein Organization

You might also read

Related Articles

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

Sort by

Same author

COX-2 inhibition improves immune system homeostasis and decreases liver damage in septic rats.

The Journal of surgical research·2009

Same author

Overexpression of violaxanthin de-epoxidase gene alleviates photoinhibition of PSII and PSI in tomato during high light and chilling stress.

Journal of plant physiology·2009

Same author

Mass spectral characterization of organophosphate-labeled, tyrosine-containing peptides: characteristic mass fragments and a new binding motif for organophosphates.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences·2009

Same author

3D-SURFER: software for high-throughput protein surface comparison and analysis.

Bioinformatics (Oxford, England)·2009

Same author

Total arch replacement with stented elephant trunk technique: a proposed treatment for complicated Stanford type B aortic dissection.

Journal of cardiac surgery·2009

Same author

Top-emitting white organic light-emitting devices with a one-dimensional metallic-dielectric photonic crystal anode.

Optics letters·2009

Search research articles

Related Experiment Video

Updated: Jul 6, 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

Fast protein tertiary structure retrieval based on global surface shape similarity.

Lee Sael¹, Bin Li, David La

¹Department of Computer Science, College of Science, Purdue University, West Lafayette, Indiana 47907, USA.

|March 26, 2008

Summary

This study introduces 3D Zernike descriptors for fast protein structure comparison. This novel method enables real-time protein structure searches, significantly improving database analysis speed.

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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jul 6, 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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Structural biology
Bioinformatics
Computational chemistry

Background:

Protein structure similarity searches are crucial for understanding protein function and evolution.
Expanding protein databases necessitate faster comparison methods.
Conventional methods based on main-chain orientation are too slow for real-time database searches.

Purpose of the Study:

To develop a computationally efficient method for protein structure comparison.
To represent protein structures compactly using a global surface shape descriptor.
To enable real-time protein structure similarity searches.

Main Methods:

Utilized three-dimensional (3D) Zernike descriptors for global surface shape representation.
Represented protein structures as a compact series expansion of 3D functions.
Benchmarked 3D Zernike descriptor performance against combinatorial extension algorithm classifications.

Main Results:

Achieved search speeds of less than a minute for databases of a few thousand structures.
Demonstrated high agreement between 3D Zernike descriptor surface representation and main-chain based representations.
Retrieved proteins of the same conformation with 89.6% accuracy within the top five closest structures.

Conclusions:

3D Zernike descriptors offer a significant speed improvement for protein structure searches.
This method facilitates large-scale global and local protein surface shape comparisons in real-time.
The approach opens new possibilities for structural genomics and protein analysis.